├── .gitignore ├── README.md ├── datasets ├── Anderson_2013 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Ballesteros_2019 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Becker_2016 │ ├── Find Results │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Bergsten_2013 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Borowiec_2015 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Branstetter_2017 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Broughton_2013 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Brown_2012 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Cannon_2016_aa │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Cannon_2016_dna │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Chen_2015 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Cognato_2001 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Crawford_2012 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Day_2013 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Devitt_2013 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Dornburg_2012 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Faircloth_2013 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Fong_2012 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Horn_2014 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Irisarri_2017 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Jarvis_2015 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Kawahara_2013 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Lartillot_2012 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Leache_2015 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Looney_2016 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── McCormack_2013 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Meiklejohn_2016 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Misof_2014 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Moyle_2016 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Murray_2013 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Near_2013 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Nguyen_2016a │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Nguyen_2016b │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Nguyen_2016c │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Nguyen_2016d │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Nguyen_2016e │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Nguyen_2016f │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Oaks_2011 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Prebus_2017 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Pyron_2011 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Ran_2018_aa │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Ran_2018_dna │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Reddy_2017 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Richart_2015 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Rightmyer_2013 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Sauquet_2011 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Seago_2011 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Sharanowski_2011 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Shen_2018 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Siler_2013 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Smith_2014 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Tolley_2013 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Unmack_2013 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Varga_2019 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Wainwright_2012 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Whelan_2017 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Wood_2012 │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Worobey_2014a │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Worobey_2014b │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Worobey_2014c │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Worobey_2014d │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Worobey_2014e │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Worobey_2014f │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Worobey_2014g │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Worobey_2014h │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── Wu_2018_aa │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt └── Wu_2018_dna │ ├── README.yaml │ ├── alignment.nex-seq-summary.txt │ └── alignment.nex-summary.txt ├── license.txt ├── new_dataset_files ├── README.md └── README.yaml ├── summary.csv └── utility_scripts ├── AMAS.py ├── README.md ├── charpartition_generator.py ├── check_files.py ├── concatenate_loci.py ├── convert_to_nexus.py ├── generate_csv.py ├── generate_summaries.py ├── gzip_datasets.py ├── split_files.sh ├── split_into_loci.py ├── translate_alignments.py └── util_functions.py /.gitignore: -------------------------------------------------------------------------------- 1 | *.DS_Store 2 | *.pyc 3 | zips/* 4 | *.nex 5 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # BenchmarkAlignments 2 | 3 | ## What's this? 4 | 5 | A curated repository of DNA and amino acid alignments with comprehensive metadata. 6 | 7 | ## What's it for? 8 | 9 | To test, verify, benchmark, and compare software and methods in phylogenetics. 10 | 11 | ## How many datasets, how big? 12 | 13 | Check out the `summary.csv` file in this repository. It has most of the data you might want on all of the alignments in the database. You can view it straight on github by just clicking on it above. 14 | 15 | As of April 2019, the database contains: 16 | 17 | * 67 datasets 18 | * 66,932 partitions 19 | * 31,971,550 alignment columns 20 | * 2,623,278,645 total alignment matrix cells 21 | 22 | ## Getting the data 23 | 24 | The data are stored on figShare, and the total download size is roughly 1GB. 25 | 26 | You can download it by hand by clicking 'Download All' at this link: https://figshare.com/s/622e9e0a156e5233944b, and then extracting each of the `.tar.gz` files yourself. 27 | 28 | If you are comfortable with the commandline, you can do it like this 29 | 30 | ```{shell} 31 | # make the directory to keep it in 32 | mkdir BenchmarkAlignments 33 | cd BenchmarkAlignemnts 34 | 35 | # download and unzip the data 36 | curl https://ndownloader.figshare.com/articles/7092356?private_link=622e9e0a156e5233944b > BenchmarkAlignments.zip 37 | unzip BenchmarkAlignments.zip 38 | 39 | # unpack the .tar.gz files 40 | find . -name "*.tar.gz" -exec tar xzf {} \; 41 | 42 | # clean up 43 | rm *.tar.gz 44 | rm *.zip 45 | ``` 46 | 47 | You should now have a series of folders named e.g. `Anderson_2013`. This is the database. 48 | 49 | # What's in each folder? 50 | 51 | Inside each folder is: 52 | 53 | 1. **`README.yaml`**: a YAML file which has metadata on the alignment including but not limited to: the license, DOIs for the original study and the dataset, notes on the dataset itself. 54 | 55 | 2. **`alignment.nex`**: a nexus formatted alignment file that contains the sequence alignment in non-interleaved nexus format, plus a SETS block which contains information on partitions, genomes, and outgroups. 56 | 57 | 3. **`alignment.nex-summary.txt`**: summary stats on the whole alignment generated by [AMAS](https://github.com/marekborowiec/AMAS). 58 | 59 | 4. **`alignment.nex-seq-summary.txt`**: summary stats on each sequence in the alignment generated by [AMAS](https://github.com/marekborowiec/AMAS). 60 | 61 | 62 | # Can I use these datasets? 63 | Yes. All of the original datasets are publicly available and can be re-used. The datasets themselves are all released under a CC0 or CCBY license. 64 | 65 | Everything here and on figShare that is not a dataset (e.g. the `summary.csv` file, `README.yaml`, the code here) is released under a CC-BY license. 66 | 67 | # Attribution 68 | 69 | If you use any of the datasets, please make sure to reference three things: 70 | 71 | 1. The original study (the full reference and DOI are provided in `README.yaml` and in `summary.csv`) 72 | 73 | 2. The dataset itself (the DOI is provided in `README.yaml` and in `summary.csv`) 74 | 75 | 3. This repository (github.com/roblanf/BenchmarkAlignments) 76 | 77 | This is essential to reward and acknowledge those who spend weeks and months in the field, laboriously chasing frogs/flies/lizards etc., then are kind enough to share their data with the world so that people like me (and you, if you're reading this) can re-use them for other things. 78 | 79 | # I want individual loci, not concatenated alignments 80 | 81 | Depending on what you're doing, you might be more interested in single-locus alignments rather than concatenated multi-locus alignments. If this is the case, please use the script `split_into_loci.py` (in the `utility_scripts` folder), as follows: 82 | 83 | ```{shell} 84 | python3 split_into_loci.py -i 'INPUT_FOLDER' -o 'OUTPUT_FOLDER' 85 | ``` 86 | 87 | Your output folder will now contain a series of single-locus alignments, with the name of the dataset prepended to the locus name (which is itself taken from the concatenated alignment file): 88 | 89 | ``` 90 | Anderson_2013_16S 91 | Anderson_2013_COI 92 | Seago_2011_28S 93 | Seago_2011_COI 94 | Seago_2011_COII 95 | ``` 96 | 97 | Note that this script will only work properly on alignments from this database, because all of the loci and other character sets in the nexus files are named with a consistent naming scheme upon which the script relies. This script will recursively search for alignments in the `INPUT_FOLDER`, and then output each locus to a new nexus file in the `OUTPUT_FOLDER`. There are two differences between the charsets in the nexus file and the single locus alignments in the `OUTPUT_FOLDER`: 98 | 99 | 1. Protein coding loci in the original files are split into 1st, 2nd, and 3rd codon positions. These are concatenated into single alignments in the output folder. (Note that they will be concatenated in no particular order). 100 | 101 | 2. Genome charsets (which are present in the original alignments) are ignored 102 | 103 | One thing to note is that the meaning of a 'locus' differs somewhat (and unavoidably) between datatsets. For example, in many datasets a 'locus' corresponds to a single transcript (i.e. multiple exons). But in other datasets, a 'locus' corresponds to a single exon. You can find more information on all of this by studying the alignments themselves, and by reading the original papers describing the study. The reference and DOI for each original study is given in the `readme.YAML` file in each folder, and in the `summary.csv` file on this repository. 104 | 105 | # I have something to say 106 | 107 | If you find errors, bugs, or have suggested datasets or features, please leave suggestions on the issue tracker here: https://github.com/roblanf/BenchmarkAlignments/issues -------------------------------------------------------------------------------- /datasets/Anderson_2013/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Anderson FE, Bergman A, Cheng SH, Pankey MS, Valinassab T. Lights out: the evolution of bacterial bioluminescence in Loliginidae. Hydrobiologia. 2014 Mar 1;725(1):189-203." 3 | year: 2014 4 | DOI: dx.doi.org/10.1007/s10750-013-1599-1 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.93s3n 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 145 12 | nchar: 3037 13 | datatype: nucleotide 14 | partitions: 4 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: no 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: "Loliginidae" 28 | english: "pencil squids" 29 | taxon ID: 6615 30 | notes: NA -------------------------------------------------------------------------------- /datasets/Anderson_2013/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 145 3037 440365 258529 58.708 1077 0.355 643 0.212 0.683 0.317 56387 26925 30414 68098 1 1 5 1 1 3 0 0 0 0 0 0 0 258509 20 -------------------------------------------------------------------------------- /datasets/Ballesteros_2019/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Ballesteros JA, Sharma PP (2019) A critical appraisal of the placement of Xiphosura (Chelicerata) with account of known sources of phylogenetic error. Systematic Biology, online in advance of print." 3 | year: 2019 4 | DOI: dx.doi.org/10.1093/sysbio/syz011 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.2g1f4n5 8 | license: "CC0" 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 53 12 | nchar: 1484206 13 | datatype: protein 14 | partitions: 3534 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 530 mya 25 | study root age: NA 26 | study clade: 27 | latin: Chelicerata 28 | english: Sea spiders, arachnids, and others 29 | taxon ID: 6843 30 | notes: NA 31 | -------------------------------------------------------------------------------- /datasets/Ballesteros_2019/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 53 1484206 78662918 43706563 55.562 1153004 0.777 895536 0.603 2211958 711976 1954362 2422327 1472509 1998340 888703 2066944 2378634 3458231 854889 1547019 1573568 1448890 1844062 2437366 1819355 2288574 427578 1151070 0 0 0 1787 0 0 5356308 38348468 -------------------------------------------------------------------------------- /datasets/Becker_2016/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Becker EA, Yao AI, Seitzer PM, Kind T, Wang T, Eigenheer R, Shao KSY, Yarov-Yarovoy V, Facciotti MT (2016) A large and phylogenetically diverse class of type 1 opsins lacking a canonical retinal binding site. PLOS ONE 11(6): e0156543." 3 | year: 2016 4 | DOI: dx.doi.org/10.1371/journal.pone.0156543 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.963hr 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 170 12 | nchar: 217 13 | datatype: protein 14 | partitions: 1 15 | genomes: 16 | mitochondrial: no 17 | nuclear: no 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: yes 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: Halobacteriacea 28 | english: halophytic bacteria 29 | taxon ID: 2236 30 | notes: NA 31 | -------------------------------------------------------------------------------- /datasets/Becker_2016/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 170 217 36890 2420 6.56 215 0.991 210 0.968 4399 163 871 796 1884 3436 110 2227 474 5682 791 394 849 297 1291 1735 2596 3811 1141 1523 0 0 0 0 0 0 2420 0 -------------------------------------------------------------------------------- /datasets/Bergsten_2013/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Bergsten J, Nilsson AN, Ronquist F. Bayesian tests of topology hypotheses with an example from diving beetles. Systematic biology. 2013 Sep 1;62(5):660-73." 3 | year: 2013 4 | DOI: dx.doi.org/10.1093/sysbio/syt029 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.s631d 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 38 12 | nchar: 2111 13 | datatype: nucleotide 14 | partitions: 8 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: "Dytiscidae" 28 | english: "diving beetles" 29 | taxon ID: 50515 30 | notes: NA -------------------------------------------------------------------------------- /datasets/Bergsten_2013/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex Andex_insignis 2111 24 1.137 0.603 0.397 601 411 418 657 0 0 0 0 0 0 0 0 0 0 0 0 0 24 0 3 | alignment.nex Canthyporus_hottentotus 2111 22 1.042 0.594 0.406 591 429 419 650 0 0 0 0 0 0 0 0 0 0 0 0 0 22 0 4 | alignment.nex Heterosternusa_pulcher 2111 17 0.805 0.607 0.393 619 406 416 653 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 5 | alignment.nex Hovahydrus_minutissimus 2111 15 0.711 0.598 0.402 599 426 416 655 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 6 | alignment.nex Hydrocolus_sahlbergi 2111 19 0.9 0.604 0.396 621 416 413 642 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 7 | alignment.nex Hydroporus_appalachius 2111 31 1.468 0.617 0.383 622 392 403 660 0 1 0 2 0 0 0 0 0 0 0 0 0 31 0 8 | alignment.nex Hydroporus_axillaris 2111 16 0.758 0.608 0.392 621 410 412 652 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 9 | alignment.nex Hydroporus_carri 2111 32 1.516 0.614 0.386 620 400 400 654 0 0 4 1 0 0 0 0 0 0 0 0 0 32 0 10 | alignment.nex Hydroporus_erythrocephalus 2111 32 1.516 0.607 0.393 623 408 409 637 0 0 2 0 0 0 0 0 0 0 0 0 0 32 0 11 | alignment.nex Hydroporus_fortis 2111 131 6.206 0.605 0.395 579 388 395 618 0 0 0 0 0 0 0 0 0 0 0 0 0 131 0 12 | alignment.nex Hydroporus_kraatzii 2111 63 2.984 0.613 0.387 614 390 402 639 1 0 1 1 0 0 0 0 0 0 0 0 0 63 0 13 | alignment.nex Hydroporus_lapponum 2111 16 0.758 0.612 0.388 633 407 405 649 0 0 0 1 0 0 0 0 0 0 0 0 0 16 0 14 | alignment.nex Hydroporus_longiusculus 2111 19 0.9 0.614 0.386 624 404 403 660 0 0 1 0 0 0 0 0 0 0 0 0 0 19 0 15 | alignment.nex Hydroporus_mannerheimi 2111 15 0.711 0.614 0.386 628 401 406 656 1 1 0 3 0 0 0 0 0 0 0 0 0 15 0 16 | alignment.nex Hydroporus_memnonius 2111 16 0.758 0.602 0.398 614 408 426 647 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 17 | alignment.nex Hydroporus_neglectus 2111 127 6.016 0.604 0.396 584 395 390 615 0 0 0 0 0 0 0 0 0 0 0 0 0 127 0 18 | alignment.nex Hydroporus_nigellus 2111 89 4.216 0.609 0.391 598 399 391 634 0 0 0 0 0 0 0 0 0 0 0 0 0 89 0 19 | alignment.nex Hydroporus_niger 2111 160 7.579 0.604 0.396 578 384 388 601 0 0 0 0 0 0 0 0 0 0 0 0 0 160 0 20 | alignment.nex Hydroporus_nigrita 2111 15 0.711 0.599 0.401 610 421 418 645 0 0 0 2 0 0 0 0 0 0 0 0 0 15 0 21 | alignment.nex Hydroporus_notabilis 2111 68 3.221 0.605 0.395 605 403 404 629 0 0 2 0 0 0 0 0 0 0 0 0 0 68 0 22 | alignment.nex Hydroporus_obscurus 2111 16 0.758 0.618 0.382 629 400 400 664 0 0 0 2 0 0 0 0 0 0 0 0 0 16 0 23 | alignment.nex Hydroporus_pilosus 2111 15 0.711 0.603 0.397 616 418 414 648 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 24 | alignment.nex Hydroporus_puberulus 2111 31 1.468 0.608 0.392 627 412 402 638 0 1 0 0 0 0 0 0 0 0 0 0 0 31 0 25 | alignment.nex Hydroporus_pubescens 2111 15 0.711 0.607 0.393 617 412 411 656 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 26 | alignment.nex Hydroporus_rufifrons 2111 76 3.6 0.615 0.385 604 394 390 647 0 0 0 0 0 0 0 0 0 0 0 0 0 76 0 27 | alignment.nex Hydroporus_scalesianus 2111 16 0.758 0.611 0.389 632 409 406 648 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 28 | alignment.nex Hydroporus_sinuatipes 2111 191 9.048 0.595 0.405 558 386 392 583 1 0 0 0 0 0 0 0 0 0 0 0 0 191 0 29 | alignment.nex Hydroporus_submuticus 2111 16 0.758 0.617 0.383 635 401 402 657 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 30 | alignment.nex Hydroporus_tessellatus 2111 18 0.853 0.599 0.401 607 416 419 641 0 1 3 5 1 0 0 0 0 0 0 0 0 18 0 31 | alignment.nex Hydroporus_tristis 2111 84 3.979 0.599 0.401 585 411 402 629 0 0 0 0 0 0 0 0 0 0 0 0 0 84 0 32 | alignment.nex Hydroporus_vagepictus 2111 15 0.711 0.597 0.403 608 421 423 644 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 33 | alignment.nex Hyphydrus_ovatus 2111 14 0.663 0.599 0.401 613 420 421 643 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 34 | alignment.nex Laccornellus_copelatoides 2111 17 0.805 0.582 0.418 597 445 430 622 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 35 | alignment.nex Neoporus_arizonicus 2111 17 0.805 0.601 0.399 616 419 417 642 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 36 | alignment.nex Neoporus_undulatus 2111 43 2.037 0.602 0.398 620 413 411 624 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 37 | alignment.nex Sanfilippodytes_terminalis 2111 15 0.711 0.6 0.4 613 414 425 644 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 38 | alignment.nex Suphrodytes_dorsalis 2111 14 0.663 0.612 0.388 624 410 403 660 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 39 | alignment.nex Suphrodytes_figuratus 2111 15 0.711 0.611 0.389 621 410 405 660 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 -------------------------------------------------------------------------------- /datasets/Bergsten_2013/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 38 2111 80218 1555 1.938 553 0.262 443 0.21 0.606 0.394 23206 15509 15507 24403 3 4 13 17 1 0 0 0 0 0 0 0 0 1555 0 -------------------------------------------------------------------------------- /datasets/Borowiec_2015/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Borowiec, M. L., Lee, E. K., Chiu, J. C., & Plachetzki, D. C. (2015). Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa. BMC genomics, 16(1), 1." 3 | year: 2015 4 | DOI: dx.doi.org/10.1186/s12864-015-2146-4 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.k6tq2 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 36 12 | nchar: 384981 13 | datatype: protein 14 | partitions: 1080 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 936.0 mya 25 | study root age: NA 26 | study clade: 27 | latin: "Metazoa" 28 | english: "metazoans" 29 | taxon ID: 33208 30 | notes: The timetree root age is for Porifera vs. other deuterostomes. -------------------------------------------------------------------------------- /datasets/Borowiec_2015/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex Acropora 384981 181128 47.049 12734 4143 11250 14218 9284 11877 5045 11234 14431 20743 4964 8124 8735 8387 10657 14742 10527 14156 2429 6173 0 0 0 0 0 0 181128 0 3 | alignment.nex Acyrthosiphon 384981 53792 13.973 17759 6909 18568 21307 14608 16800 7917 22940 25480 33634 8225 17791 13499 12394 14896 23346 17862 21440 3960 11854 0 0 0 0 0 0 53792 0 4 | alignment.nex Amphimedon 384981 106892 27.766 15837 5323 15229 19024 11240 16206 7046 16788 18806 29129 6170 11047 12469 10798 14452 22484 14818 18445 3284 9494 0 0 0 0 0 0 106892 0 5 | alignment.nex Anolis 384981 52170 13.551 22733 6821 17257 24105 14121 19337 8483 18121 22751 35503 7988 12363 15467 14543 18307 21836 16339 21974 4083 10679 0 0 0 0 0 0 52170 0 6 | alignment.nex Apis 384981 48441 12.583 19468 6687 17525 23159 14148 17112 8233 26311 26041 34564 7621 17369 13816 13342 16109 21427 18009 19121 4233 12245 0 0 0 0 0 0 48441 0 7 | alignment.nex Bombus 384981 51433 13.36 19921 6788 17644 22961 13937 16211 8381 22865 24741 34821 7800 16533 14045 13482 16616 21489 18267 20736 4216 12094 0 0 0 0 0 0 51433 0 8 | alignment.nex Branchiostoma 384981 49605 12.885 22986 6534 19121 23030 13872 20270 8738 16282 21942 33522 8912 12059 15443 15212 19059 21047 18175 24371 4204 10597 0 0 0 0 0 0 49605 0 9 | alignment.nex Brugia 384981 159980 41.555 14866 4762 12334 15132 10316 11862 5458 15391 15038 22951 5544 9607 8719 8149 13541 15029 11132 14719 2714 7729 6 0 2 0 0 0 159980 0 10 | alignment.nex Caenorhabditis 384981 129536 33.647 18019 4532 14480 17998 11626 14497 6206 15905 17955 23882 6747 10905 10293 9625 14153 16712 13394 17491 3071 7954 0 0 0 0 0 0 129536 0 11 | alignment.nex Capitella 384981 41447 10.766 23476 7076 19734 23219 15065 19224 9420 18824 23338 34700 9117 13442 15136 14537 18486 23954 17169 23095 3988 10534 0 0 0 0 0 0 41447 0 12 | alignment.nex Ciona 384981 121715 31.616 16335 5476 14655 17053 11604 14611 6751 15804 19008 26214 6824 11933 10924 10401 13211 18852 14061 18041 3206 8302 0 0 0 0 0 0 121715 0 13 | alignment.nex Danaus 384981 58448 15.182 22533 6529 17994 21747 12965 17938 8263 19550 22746 33634 7416 14260 14552 12344 17850 21609 17078 22136 4130 11259 0 0 0 0 0 0 58448 0 14 | alignment.nex Daphnia 384981 45105 11.716 22204 6646 18232 22858 14940 18960 8554 19796 22590 35869 7891 14291 14951 14373 17992 24280 17511 22983 4327 10628 0 0 0 0 0 0 45105 0 15 | alignment.nex Drosophila 384981 29468 7.654 25530 6740 19379 23913 15017 19938 9261 19884 22643 37460 8351 14866 15317 15970 20766 22641 18278 23635 4186 11738 0 0 0 0 0 0 29468 0 16 | alignment.nex Fugu 384981 69212 17.978 21575 6579 16867 21575 13143 18672 8349 15601 20050 33756 7695 11378 14474 14064 17873 21914 16271 22309 3927 9697 0 0 0 0 0 0 69212 0 17 | alignment.nex Gallus 384981 151824 39.437 16735 4937 12070 16936 9600 13477 5869 11925 15295 24794 5488 8588 10644 10221 13255 15617 11483 16067 2780 7376 0 0 0 0 0 0 151824 0 18 | alignment.nex Gasterosteus 384981 22144 5.752 25628 7463 19560 24980 14952 21974 9397 16894 22615 38567 8987 12652 16751 15823 21479 25111 18479 26090 4482 10953 0 0 0 0 0 0 22144 0 19 | alignment.nex Homo 384981 83222 21.617 21011 6067 15427 21533 12659 17867 7723 15552 19349 33199 7000 10660 14322 13559 17427 19990 14916 20229 3863 9406 0 0 0 0 0 0 83222 0 20 | alignment.nex Hydra 384981 118455 30.769 14603 5447 14738 17897 12865 13744 6075 18436 21736 26908 6075 13731 10243 10280 11619 19759 13045 17088 3042 9195 0 0 0 0 0 0 118455 0 21 | alignment.nex Ixodes 384981 103052 26.768 21391 5955 15404 18635 12060 16970 7653 11813 16589 31259 6365 9151 13373 11481 17957 18775 13947 21262 3538 8351 0 0 0 0 0 0 103052 0 22 | alignment.nex Latimeria 384981 31492 8.18 22942 7367 18058 25379 15404 20194 8832 19342 24690 37261 8505 13367 15785 15545 19098 23561 17946 24301 4386 11526 0 0 0 0 0 0 31492 0 23 | alignment.nex Lottia 384981 34415 8.939 19610 7023 20366 23841 15209 19398 8648 23035 26998 34751 8552 16033 14611 14334 16720 23784 18405 22750 4217 12281 0 0 0 0 0 0 34415 0 24 | alignment.nex Mnemiopsis 384981 111657 29.003 16793 5765 15489 18562 11381 14975 6858 16251 19888 27130 6360 12023 11530 10646 13434 20303 15009 18917 3011 8999 0 0 0 0 0 0 111657 0 25 | alignment.nex Monosiga 384981 176892 45.948 20408 3441 12234 13320 8111 12148 5824 9418 10205 21854 4936 6895 9656 9589 13769 12425 11234 14559 2398 5665 0 0 0 0 0 0 176892 0 26 | alignment.nex Nematostella 384981 68747 17.857 20606 6319 17724 21297 13859 18389 8196 17924 22360 31809 7907 12400 13891 12837 16515 21686 16438 22029 3848 10200 0 0 0 0 0 0 68747 0 27 | alignment.nex Oikopleura 384981 155811 40.472 15877 4192 13306 16554 10619 13089 5193 14540 17386 21607 5615 10056 9138 8609 12315 15566 11537 14326 2833 6812 0 0 0 0 0 0 155811 0 28 | alignment.nex Pinctada 384981 224174 58.23 9304 3067 9869 11081 6871 8848 3985 9466 12422 15240 4430 6907 6847 6724 8187 10862 8452 10884 1747 5614 0 0 0 0 0 0 224174 0 29 | alignment.nex Rhodnius 384981 262610 68.214 7124 2583 6490 8260 5396 6680 2921 7978 9079 12696 3027 5749 5258 4464 6059 8185 6262 8271 1533 4356 0 0 0 0 0 0 262610 0 30 | alignment.nex Saccoglossus 384981 57898 15.039 19867 6416 19225 22026 13643 18222 8501 19878 24190 31793 8549 13688 14014 13650 16739 22275 17430 21831 3943 11203 0 0 0 0 0 0 57898 0 31 | alignment.nex Salpingoeca 384981 154258 40.069 21639 4005 13987 14274 9267 13543 6702 10343 12539 22631 5724 7168 10406 9955 15177 14395 13214 17106 2611 6037 0 0 0 0 0 0 154258 0 32 | alignment.nex Strigamia 384981 63777 16.566 19552 6481 18013 21465 14580 16937 8022 20737 23159 32811 7590 15178 13299 12919 16449 21420 17034 21115 3888 10555 0 0 0 0 0 0 63777 0 33 | alignment.nex Strongylocentrotus 384981 92422 24.007 19473 5545 16704 20020 12410 17207 7674 16206 20229 28875 7869 11284 13017 12441 15761 20148 15398 19648 3481 9169 0 0 0 0 0 0 92422 0 34 | alignment.nex Tetranychus 384981 102305 26.574 16233 5384 16457 18553 13318 14469 6378 20687 21680 28870 6193 13972 11827 10134 13826 20615 13989 16861 3326 9904 0 0 0 0 0 0 102305 0 35 | alignment.nex Tribolium 384981 28683 7.45 21874 6943 19375 24814 15726 19295 8712 22136 27056 36961 7414 16758 15499 14364 17527 22664 18839 23989 4269 12083 0 0 0 0 0 0 28683 0 36 | alignment.nex Trichoplax 384981 70520 18.318 19600 6378 18143 19537 13616 16673 7351 22363 22361 31254 6969 15581 12208 12648 16407 22777 16136 19259 3663 11537 0 0 0 0 0 0 70520 0 37 | alignment.nex Xenopus 384981 34393 8.934 22753 7351 18327 24577 14929 20297 8966 19204 23420 37332 8451 13407 15887 15485 19033 24247 17688 23479 4368 11387 0 0 0 0 0 0 34393 0 -------------------------------------------------------------------------------- /datasets/Borowiec_2015/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 36 384981 13859316 3347123 24.151 351953 0.914 302196 0.785 688999 209674 581235 714840 452361 587911 265585 619424 730806 1077984 253271 441216 456046 433329 562721 715527 545772 704713 127185 343586 6 0 2 0 0 0 3347123 0 -------------------------------------------------------------------------------- /datasets/Branstetter_2017/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Branstetter MG, Danforth BN, Pitts JP, Faircloth BC, Ward PS, Buffington ML, Gates MW, Kula RR, Brady SG (2017) Phylogenomic Insights into the Evolution of Stinging Wasps and the Origins of Ants and Bees. Current Biology 27(7): 1019-1025." 3 | year: 2017 4 | DOI: dx.doi.org/10.1016/j.cub.2017.03.027 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.r8d4q 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 187 12 | nchar: 183747 13 | datatype: nucleotide 14 | partitions: 807 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 169 mya 25 | study root age: 170 mya 26 | study clade: 27 | latin: "Aculeata" 28 | english: Stinging wasps 29 | taxon ID: 7434 30 | notes: This is the dataset Hym-187T-F75, which is the dataset used for the main figure in the paper. One of many datasets available from the link under "Alignment supermatrices" on Dryad. 31 | -------------------------------------------------------------------------------- /datasets/Branstetter_2017/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 187 183747 34360689 7137124 20.771 145271 0.791 129078 0.702 0.538 0.462 7193878 6364888 6218181 7446618 0 0 0 0 0 0 0 0 0 0 0 0 0 2743984 4393140 -------------------------------------------------------------------------------- /datasets/Broughton_2013/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Broughton RE, Betancur RR, Li C, Arratia G, Ortí G. Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution. PLoS Curr. 2013 Apr 16;5(5)." 3 | year: 2013 4 | DOI: dx.doi.org/10.1371/currents.tol.2ca8041495ffafd0c92756e75247483e 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.f1t15 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 61 12 | nchar: 19997 13 | datatype: nucleotide 14 | partitions: 61 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 436.8 mya 25 | study root age: 427 mya 26 | study clade: 27 | latin: "Osteichthyes" 28 | english: "bony fishes" 29 | taxon ID: 117571 30 | notes: NA 31 | -------------------------------------------------------------------------------- /datasets/Broughton_2013/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 61 19997 1219817 501485 41.111 12159 0.608 10492 0.525 0.474 0.526 184346 193970 184272 155637 9 11 38 34 6 9 0 0 0 0 0 63 0 501422 0 -------------------------------------------------------------------------------- /datasets/Brown_2012/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Brown RM, Siler CD, Das I, Min Y. Testing the phylogenetic affinities of Southeast Asia’s rarest geckos: Flap-legged geckos (Luperosaurus), Flying geckos (Ptychozoon) and their relationship to the pan-Asian genus Gekko. Molecular phylogenetics and evolution. 2012 Jun 30;63(3):915-21." 3 | year: 2012 4 | DOI: dx.doi.org/10.1016/j.ympev.2012.02.019 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.7bn0fr99 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 41 12 | nchar: 1665 13 | datatype: nucleotide 14 | partitions: 7 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 84.7 mya 25 | study root age: NA 26 | study clade: 27 | latin: "Ptychozoon" 28 | english: "Asian geckos" 29 | taxon ID: 1118401 30 | notes: NA 31 | -------------------------------------------------------------------------------- /datasets/Brown_2012/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex Cyrtodactylus_annulatus_KU314944 1665 660 39.64 0.552 0.448 357 339 111 198 0 0 0 0 0 0 0 0 0 0 0 0 0 660 0 3 | alignment.nex Cyrtodactylus_philippinicus_KU304784 1665 663 39.82 0.557 0.443 351 331 113 207 0 0 0 0 0 0 0 0 0 0 0 0 0 663 0 4 | alignment.nex Gehyra_australis_AMS139934 1665 42 2.523 0.543 0.457 532 500 240 348 0 1 2 0 0 0 0 0 0 0 0 0 0 42 0 5 | alignment.nex Gehyra_mutilata_AMB7515 1665 37 2.222 0.534 0.466 497 513 246 372 0 0 0 0 0 0 0 0 0 0 0 0 0 37 0 6 | alignment.nex Gekko_athymus_RMB3118 1665 64 3.844 0.593 0.407 521 409 243 427 0 0 0 1 0 0 0 0 0 0 0 0 0 59 5 7 | alignment.nex Gekko_auriverrucosus_ZK3 1665 180 10.811 0.587 0.413 500 408 205 372 0 0 0 0 0 0 0 0 0 0 0 0 0 42 138 8 | alignment.nex Gekko_badenii_JB13 1665 45 2.703 0.585 0.415 550 431 240 396 0 2 0 0 0 1 0 0 0 0 0 0 0 44 1 9 | alignment.nex Gekko_chinensis_China_LG4210 1665 43 2.583 0.605 0.395 557 408 232 425 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 10 | alignment.nex Gekko_crombota_BabuynCl_RMB5946 1665 33 1.982 0.555 0.445 532 460 266 374 0 0 0 0 0 0 0 0 0 0 0 0 0 33 0 11 | alignment.nex Gekko_gecko_CAS204952 1665 31 1.862 0.572 0.428 520 439 260 415 0 0 0 0 0 0 0 0 0 0 0 0 0 31 0 12 | alignment.nex Gekko_grossmani_JFBM9 1665 41 2.462 0.594 0.406 576 408 251 388 0 0 0 0 0 1 0 0 0 0 0 0 0 40 1 13 | alignment.nex Gekko_hokouensis_HOFH89053103 1665 69 4.144 0.558 0.442 500 450 255 390 0 0 0 1 0 0 0 0 0 0 0 0 0 69 0 14 | alignment.nex Gekko_japonicus_HOFH10061402 1665 34 2.042 0.562 0.438 535 460 255 381 0 0 0 0 0 0 0 0 0 0 0 0 0 34 0 15 | alignment.nex Gekko_mindorensis_CDS1229 1665 37 2.222 0.594 0.406 542 417 244 425 0 0 0 0 0 0 0 0 0 0 0 0 0 37 0 16 | alignment.nex Gekko_monarchus_Palawan_ACD1278 1665 36 2.162 0.598 0.402 560 423 231 414 1 0 0 0 0 0 0 0 0 0 0 0 0 36 0 17 | alignment.nex Gekko_petricolis_JB70 1665 43 2.583 0.588 0.412 532 426 242 422 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 18 | alignment.nex Gekko_romblon_Tablas_RMB8789 1665 32 1.922 0.585 0.415 552 432 245 404 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 19 | alignment.nex Gekko_smithii_Wmalaysia_LG6095 1665 24 1.441 0.584 0.416 546 445 237 413 0 0 0 0 0 0 0 0 0 0 0 0 0 24 0 20 | alignment.nex Gekko_subpalmatus_AMB5567 1665 49 2.943 0.593 0.407 539 418 239 419 0 0 1 0 0 0 0 0 0 0 0 0 0 49 0 21 | alignment.nex Gekko_swinhonis_ZK5 1665 55 3.303 0.58 0.42 532 430 247 401 0 0 0 0 0 0 0 0 0 0 0 0 0 49 6 22 | alignment.nex Gekko_vittatus_JAM2171 1665 43 2.583 0.617 0.383 558 382 239 443 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 23 | alignment.nex Gekko_vittatus_USNM533255 1665 41 2.462 0.619 0.381 557 384 234 449 0 0 0 0 0 0 0 0 0 0 0 0 0 41 0 24 | alignment.nex Hemidactylus_bowringii_EU268373 1665 482 28.949 0.57 0.43 404 375 133 270 0 0 0 1 0 0 0 0 0 0 0 0 0 482 0 25 | alignment.nex Lepidodactylus_herrei_RMB4330 1665 451 27.087 0.56 0.44 389 380 154 291 0 0 0 0 0 0 0 0 0 0 0 0 0 451 0 26 | alignment.nex Lepidodactylus_moestus_USNM521730 1665 43 2.583 0.546 0.454 509 482 255 376 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 27 | alignment.nex Luperosaurus_Palawan_ELR1579 1665 1247 74.895 0.536 0.464 112 80 114 112 0 0 0 0 0 0 0 0 0 0 0 0 0 1247 0 28 | alignment.nex Luperosaurus_angliit_ASCOT_ACD3678 1665 28 1.682 0.561 0.439 527 459 258 388 0 0 1 3 0 1 0 0 0 0 0 0 0 28 0 29 | alignment.nex Luperosaurus_cumingii_Bicol_RMB3546 1665 456 27.387 0.596 0.404 430 356 133 290 0 0 0 0 0 0 0 0 0 0 0 0 0 456 0 30 | alignment.nex Luperosaurus_iskandari_RMB1653 1665 410 24.625 0.599 0.401 416 296 207 335 0 0 0 1 0 0 0 0 0 0 0 0 0 410 0 31 | alignment.nex Luperosaurus_joloensis_Mindanao_RMB9416 1665 291 17.477 0.558 0.442 461 426 181 306 0 0 0 0 0 0 0 0 0 0 0 0 0 291 0 32 | alignment.nex Luperosaurus_macgregori_BabynClro_RMB5918 1665 27 1.622 0.567 0.433 530 449 261 398 0 0 0 0 0 0 0 0 0 0 0 0 0 27 0 33 | alignment.nex Luperosaurus_macgregori_Batanes_RMB9042 1665 26 1.562 0.564 0.436 534 456 258 391 0 0 0 0 0 0 0 0 0 0 0 0 0 26 0 34 | alignment.nex Luperosaurus_sp_ACD6021 1665 26 1.562 0.564 0.436 529 456 259 395 0 0 0 0 0 0 0 0 0 0 0 0 0 26 0 35 | alignment.nex Lygodactylus_bradfieldi_EU423279 1665 450 27.027 0.54 0.46 395 414 145 261 0 0 0 0 0 0 0 0 0 0 0 0 0 450 0 36 | alignment.nex Phelsuma_serraticauda_EU423296 1665 447 26.847 0.617 0.383 422 342 125 328 0 0 0 0 0 1 0 0 0 0 0 0 0 447 0 37 | alignment.nex Pseudogekko_compressicorpus_CDS5000 1665 29 1.742 0.559 0.441 501 458 263 413 0 0 0 0 0 1 0 0 0 0 0 0 0 29 0 38 | alignment.nex Pseudogekko_smaragdinus_CDS1050 1665 27 1.622 0.548 0.452 505 471 269 393 0 0 0 0 0 0 0 0 0 0 0 0 0 27 0 39 | alignment.nex Ptychozoon_khuli_Tioman_4679 1665 43 2.583 0.547 0.453 488 449 285 400 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 40 | alignment.nex Ptychozoon_lionotum_Thailand_DSM798M 1665 42 2.523 0.547 0.453 503 466 270 384 0 0 0 0 0 0 0 0 0 0 0 0 0 42 0 41 | alignment.nex Ptychozoon_racophorus_P0500 1665 33 1.982 0.539 0.461 505 473 280 374 0 0 0 0 0 0 0 0 0 0 0 0 0 33 0 42 | alignment.nex Tarentola_mauritanica_EU443255 1665 659 39.58 0.55 0.45 339 343 110 214 0 0 0 0 0 0 0 0 0 0 0 0 0 659 0 -------------------------------------------------------------------------------- /datasets/Brown_2012/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 41 1665 68265 7519 11.014 1028 0.617 891 0.535 0.571 0.429 19945 16944 9035 14802 1 3 4 7 0 5 0 0 0 0 0 0 0 7368 151 -------------------------------------------------------------------------------- /datasets/Cannon_2016_aa/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Cannon JT, Vellutini BC, Smith J, Ronquist F, Jondelius U, Hejnol A (2016) Xenacoelomorpha is the sister group to Nephrozoa. Nature 530(7588): 89–93. http://dx.doi.org/10.1038/nature16520" 3 | year: 2016 4 | DOI: dx.doi.org/10.1038/nature16520 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.493b7 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 78 12 | nchar: 44896 13 | datatype: protein 14 | partitions: 212 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 952 mya 25 | study root age: NA 26 | study clade: 27 | latin: Metazoa 28 | english: Animals 29 | taxon ID: 33208 30 | notes: This dataset (78 taxa, 212 loci) is referred to as the 'primary' dataset in the ms, and forms the basis of Figure 2 in the ms. This is the amino acid dataset (212_78_MB_aa.nex) taken from the 'supplementary mrbayes files' link in the Dryad repository (http://datadryad.org/bitstream/handle/10255/dryad.107232/supplementarymrbayesfiles.zip?sequence=1). There is a nucleotide (1st and 2nd positions only) version of this dataset stored in this repository as Cannon_2016a. 31 | -------------------------------------------------------------------------------- /datasets/Cannon_2016_aa/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 78 44896 3501888 1088721 31.09 37164 0.828 30646 0.683 160005 52311 134011 145690 115220 142959 63635 151850 159526 255301 61255 94738 99001 87594 131457 146569 118628 173596 32143 87678 0 0 0 0 0 0 1088721 0 -------------------------------------------------------------------------------- /datasets/Cannon_2016_dna/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Cannon JT, Vellutini BC, Smith J, Ronquist F, Jondelius U, Hejnol A (2016) Xenacoelomorpha is the sister group to Nephrozoa. Nature 530(7588): 89–93. http://dx.doi.org/10.1038/nature16520" 3 | year: 2016 4 | DOI: dx.doi.org/10.1038/nature16520 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.493b7 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 78 12 | nchar: 89792 13 | datatype: nucleotide 14 | partitions: 424 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 952 mya 25 | study root age: NA 26 | study clade: 27 | latin: Metazoa 28 | english: Animals 29 | taxon ID: 33208 30 | notes: This dataset (78 taxa, 212 loci) is referred to as the 'primary' dataset in the ms, and forms the basis of Figure 2 in the ms. This is the nucleotide dataset (212_78_MB_nuc.nex) taken from the 'supplementary mrbayes files' link in the Dryad repository (http://datadryad.org/bitstream/handle/10255/dryad.107232/supplementarymrbayesfiles.zip?sequence=1). CHARSETS were added according to the CHARSETS from the protein version of this dataset, which is stored in this repository as Cannon_2016b. 31 | -------------------------------------------------------------------------------- /datasets/Cannon_2016_dna/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 78 89792 7003776 2177442 31.09 61944 0.69 47729 0.532 0.575 0.425 1358869 627864 1115131 1044574 0 131457 0 255301 146569 146569 0 0 0 0 0 0 0 2177442 0 -------------------------------------------------------------------------------- /datasets/Chen_2015/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Chen MY, Liang D, Zhang P (2015) Selecting question-specific genes to reduce incongruence in phylogenomics: a case study of jawed vertebrate backbone phylogeny. Systematic Biology 64(6): 1104-1120." 3 | year: 2015 4 | DOI: dx.doi.org/10.1093/sysbio/syv059 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.47v40 8 | license: "CC0" 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 58 12 | nchar: 1806035 13 | datatype: protein 14 | partitions: 4682 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 473 mya 25 | study root age: 'NA' 26 | study clade: 27 | latin: Gnathostomata 28 | english: Jawed vertebrates 29 | taxon ID: 7776 30 | notes: This is the dataset named "total_evidence_4682gene_Pro.nex" from the repository. The original paper filtered this data in many interesting ways. -------------------------------------------------------------------------------- /datasets/Chen_2015/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 58 1806035 104750030 22063606 21.063 1195041 0.662 876162 0.485 5407618 1717936 4388012 6122028 3277392 4620491 2179263 4225371 5485908 8556165 1997335 3245861 3936491 3947100 4492162 5934322 4222976 5359790 1009437 2560766 0 0 0 0 0 0 156936 21906670 -------------------------------------------------------------------------------- /datasets/Cognato_2001/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Cognato AI, Vogler AP. Exploring data interaction and nucleotide alignment in a multiple gene analysis of Ips (Coleoptera: Scolytinae). Systematic Biology. 2001 Nov 1;50(6):758-80." 3 | year: 2001 4 | DOI: dx.doi.org/10.1080/106351501753462803 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.678 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 44 12 | nchar: 1897 13 | datatype: nucleotide 14 | partitions: 7 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: "Coleoptera: Scolytinae" 28 | english: "Bark beetles" 29 | taxon ID: 55867 30 | notes: Morphological characters were removed from the alignment -------------------------------------------------------------------------------- /datasets/Cognato_2001/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex Ac1 1897 106 5.588 0.66 0.34 569 327 282 613 0 0 0 0 0 0 0 0 0 0 0 0 0 104 2 3 | alignment.nex Am1 1897 390 20.559 0.668 0.332 486 279 221 521 0 0 0 0 0 0 0 0 0 0 0 0 0 100 290 4 | alignment.nex Av5 1897 88 4.639 0.663 0.337 579 326 283 621 0 0 0 0 0 0 0 0 0 0 0 0 0 82 6 5 | alignment.nex Bon2 1897 118 6.22 0.652 0.348 551 327 292 609 0 0 0 0 0 0 0 0 0 0 0 0 0 100 18 6 | alignment.nex Bor2 1897 100 5.271 0.663 0.337 568 323 283 623 0 0 0 0 0 0 0 0 0 0 0 0 0 98 2 7 | alignment.nex Cala2 1897 100 5.271 0.663 0.337 570 320 286 621 0 0 0 0 0 0 0 0 0 0 0 0 0 97 3 8 | alignment.nex Cali1 1897 101 5.324 0.661 0.339 570 322 287 617 0 0 0 0 0 0 0 0 0 0 0 0 0 98 3 9 | alignment.nex Ce3 1897 102 5.377 0.657 0.343 568 332 284 611 0 0 0 0 0 0 0 0 0 0 0 0 0 100 2 10 | alignment.nex Co4 1897 98 5.166 0.669 0.331 581 318 277 623 0 0 0 0 0 0 0 0 0 0 0 0 0 95 3 11 | alignment.nex Con3 1897 361 19.03 0.643 0.357 484 304 245 503 0 0 0 0 0 0 0 0 0 0 0 0 0 110 251 12 | alignment.nex Cr2 1897 108 5.693 0.661 0.339 567 322 285 615 0 0 0 0 0 0 0 0 0 0 0 0 0 93 15 13 | alignment.nex Du3 1897 102 5.377 0.656 0.344 568 334 284 609 0 0 0 0 0 0 0 0 0 0 0 0 0 100 2 14 | alignment.nex Em1 1897 97 5.113 0.653 0.347 562 331 293 614 0 0 0 0 0 0 0 0 0 0 0 0 0 95 2 15 | alignment.nex Gr2 1897 118 6.22 0.662 0.338 567 321 280 611 0 0 0 0 0 0 0 0 0 0 0 0 0 101 17 16 | alignment.nex Ho5 1897 98 5.166 0.668 0.332 575 312 285 627 0 0 0 0 0 0 0 0 0 0 0 0 0 96 2 17 | alignment.nex Hu2 1897 103 5.43 0.656 0.344 559 334 283 618 0 0 0 0 0 0 0 0 0 0 0 0 0 98 5 18 | alignment.nex Int7 1897 47 2.478 0.67 0.33 589 330 280 651 0 0 0 0 0 0 0 0 0 0 0 0 0 45 2 19 | alignment.nex Knu1 1897 99 5.219 0.655 0.345 558 327 293 620 0 0 0 0 0 0 0 0 0 0 0 0 0 97 2 20 | alignment.nex Lat3 1897 94 4.955 0.633 0.367 548 364 297 594 0 0 0 0 0 0 0 0 0 0 0 0 0 92 2 21 | alignment.nex Le3 1897 100 5.271 0.652 0.348 561 337 288 611 0 0 0 0 0 0 0 0 0 0 0 0 0 98 2 22 | alignment.nex Lo3 1897 746 39.325 0.683 0.317 357 213 152 429 0 0 0 0 0 0 0 0 0 0 0 0 0 97 649 23 | alignment.nex Ma1 1897 743 39.167 0.69 0.31 365 212 146 431 0 0 0 0 0 0 0 0 0 0 0 0 0 96 647 24 | alignment.nex Mo1 1897 98 5.166 0.656 0.344 568 330 289 612 0 0 0 0 0 0 0 0 0 0 0 0 0 96 2 25 | alignment.nex Mx1 1897 359 18.925 0.627 0.373 484 327 247 480 0 0 0 0 0 0 0 0 0 0 0 0 0 108 251 26 | alignment.nex Nob1 1897 745 39.273 0.688 0.312 372 216 144 420 0 0 0 0 0 0 0 0 0 0 0 0 0 98 647 27 | alignment.nex Oer1 1897 102 5.377 0.647 0.353 552 350 284 609 0 0 0 0 0 0 0 0 0 0 0 0 0 100 2 28 | alignment.nex Ort1 1897 105 5.535 0.662 0.338 559 317 289 627 0 0 0 0 0 0 0 0 0 0 0 0 0 95 10 29 | alignment.nex Pa2 1897 97 5.113 0.661 0.339 572 325 285 618 0 0 0 0 0 0 0 0 0 0 0 0 0 95 2 30 | alignment.nex Pet1 1897 99 5.219 0.657 0.343 563 334 283 618 0 0 0 0 0 0 0 0 0 0 0 0 0 97 2 31 | alignment.nex Pho1 1897 104 5.482 0.651 0.349 554 332 293 614 0 0 0 0 0 0 0 0 0 0 0 0 0 94 10 32 | alignment.nex Pica1 1897 743 39.167 0.701 0.299 375 192 153 434 0 0 0 0 0 0 0 0 0 0 0 0 0 96 647 33 | alignment.nex Pil2 1897 100 5.271 0.663 0.337 570 323 282 622 0 0 0 0 0 0 0 0 0 0 0 0 0 98 2 34 | alignment.nex Pin1 1897 75 3.954 0.678 0.322 591 308 278 645 0 0 0 0 0 0 0 0 0 0 0 0 0 73 2 35 | alignment.nex Pito1 1897 95 5.008 0.639 0.361 550 358 293 601 0 0 0 0 0 0 0 0 0 0 0 0 0 93 2 36 | alignment.nex Pk1 1897 94 4.955 0.647 0.353 572 338 298 595 0 0 0 0 0 0 0 0 0 0 0 0 0 92 2 37 | alignment.nex Pl4 1897 52 2.741 0.671 0.329 592 329 278 646 0 0 0 0 0 0 0 0 0 0 0 0 0 50 2 38 | alignment.nex Pro 1897 102 5.377 0.661 0.339 562 321 287 625 0 0 0 0 0 0 0 0 0 0 0 0 0 100 2 39 | alignment.nex Sch1 1897 746 39.325 0.674 0.326 351 222 153 425 0 0 0 0 0 0 0 0 0 0 0 0 0 99 647 40 | alignment.nex Sex1 1897 98 5.166 0.658 0.342 567 333 283 616 0 0 0 0 0 0 0 0 0 0 0 0 0 96 2 41 | alignment.nex Sp1 1897 100 5.271 0.644 0.356 569 353 287 588 0 0 0 0 0 0 0 0 0 0 0 0 0 98 2 42 | alignment.nex Ste1 1897 763 40.221 0.695 0.305 359 201 145 429 0 0 0 0 0 0 0 0 0 0 0 0 0 99 664 43 | alignment.nex Tri4 1897 100 5.271 0.662 0.338 566 321 286 624 0 0 0 0 0 0 0 0 0 0 0 0 0 98 2 44 | alignment.nex Ty1 1897 99 5.219 0.651 0.349 561 343 285 609 0 0 0 0 0 0 0 0 0 0 0 0 0 97 2 45 | alignment.nex Wo3 1897 101 5.324 0.653 0.347 562 340 283 611 0 0 0 0 0 0 0 0 0 0 0 0 0 99 2 -------------------------------------------------------------------------------- /datasets/Cognato_2001/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 44 1897 83468 8996 10.778 758 0.4 648 0.342 0.661 0.339 23473 13728 11611 25660 0 0 0 0 0 0 0 0 0 0 0 0 0 4163 4833 -------------------------------------------------------------------------------- /datasets/Crawford_2012/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Crawford, N. G., Faircloth, B. C., McCormack, J. E., Brumfield, R. T., Winker, K., & Glenn, T. C. (2012). More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biology Letters, 8(5), 783-786." 3 | year: 2012 4 | DOI: dx.doi.org/10.1098/rsbl.2012.0331 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.75nv22qj 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 10 12 | nchar: 465241 13 | datatype: nucleotide 14 | partitions: 1145 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 277.8 mya 25 | study root age: NA 26 | study clade: 27 | latin: "Sauria" 28 | english: "Diapsids" 29 | taxon ID: 32561 30 | notes: NA -------------------------------------------------------------------------------- /datasets/Crawford_2012/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex alligator_mississippiensis 465241 21089 4.533 0.623 0.377 137985 83442 84088 138637 0 0 0 0 0 0 0 0 0 0 0 0 0 21089 0 3 | alignment.nex anolis_carolinensis 465241 54711 11.76 0.617 0.383 126419 78201 78915 126995 0 0 0 0 0 0 0 0 0 0 0 0 0 54711 0 4 | alignment.nex chrysemys_picta 465241 24056 5.171 0.623 0.377 137111 82860 83439 137775 0 0 0 0 0 0 0 0 0 0 0 10 0 24046 0 5 | alignment.nex crocodylus_porosus 465241 58344 12.541 0.621 0.379 126082 76740 77369 126706 0 0 0 0 0 0 0 0 0 0 0 0 0 58344 0 6 | alignment.nex gallus_gallus 465241 15826 3.402 0.618 0.382 138557 85416 86104 139338 0 0 0 0 0 0 0 0 0 0 0 0 0 15826 0 7 | alignment.nex homo_sapiens 465241 15633 3.36 0.613 0.387 137459 86608 87319 138222 0 0 0 0 0 0 0 0 0 0 0 0 0 15633 0 8 | alignment.nex pantherophis_guttata 465241 27336 5.876 0.619 0.381 135061 83159 83794 135891 0 0 0 0 0 0 0 0 0 0 0 7 0 27329 0 9 | alignment.nex pelomedusa_subrufa 465241 113864 24.474 0.617 0.383 108132 67227 67377 108641 0 0 0 0 0 0 0 0 0 0 0 0 0 113864 0 10 | alignment.nex sphenodon_tuatara 465241 128643 27.651 0.615 0.385 103378 64648 64830 103742 0 0 0 0 0 0 0 0 0 0 0 0 0 128643 0 11 | alignment.nex zebra_finch 465241 15406 3.311 0.619 0.381 138882 85350 85897 139706 0 0 0 0 0 0 0 0 0 0 0 309 0 15097 0 -------------------------------------------------------------------------------- /datasets/Crawford_2012/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 10 465241 4652410 474908 10.208 86887 0.187 27844 0.06 0.618 0.382 1289066 793651 799132 1295653 0 0 0 0 0 0 0 0 0 0 0 326 0 474582 0 -------------------------------------------------------------------------------- /datasets/Day_2013/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Day JJ, Peart CR, Brown KJ, Friel JP, Bills R, Moritz T. Continental diversification of an African catfish radiation (Mochokidae: Synodontis). Systematic biology. 2013 Jan 9:syt001." 3 | year: 2013 4 | DOI: dx.doi.org/10.1093/sysbio/syt001 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.b6225 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 152 12 | nchar: 3586 13 | datatype: nucleotide 14 | partitions: 11 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 18.5 mya 25 | study root age: NA 26 | study clade: 27 | latin: "Synodontis" 28 | english: "African catfish" 29 | taxon ID: 42509 30 | notes: NA 31 | -------------------------------------------------------------------------------- /datasets/Day_2013/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 152 3586 545072 99875 18.323 1343 0.375 999 0.279 0.53 0.47 118198 120814 88615 117445 5 21 40 37 11 11 0 0 0 0 0 321 0 99554 0 -------------------------------------------------------------------------------- /datasets/Devitt_2013/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Devitt TJ, Devitt SE, Hollingsworth BD, McGuire JA, Moritz C. Montane refugia predict population genetic structure in the Large‐blotched Ensatina salamander. Molecular ecology. 2013 Mar 1;22(6):1650-65." 3 | year: 2013 4 | DOI: dx.doi.org/10.1111/mec.12196 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.k9g50 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 69 12 | nchar: 823 13 | datatype: nucleotide 14 | partitions: 4 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: no 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: "Ensatina eschscholtzii klauberi" 28 | english: "Large-blotched Ensatina salamander" 29 | taxon ID: 58674 30 | notes: NA 31 | -------------------------------------------------------------------------------- /datasets/Devitt_2013/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 69 823 56787 77 0.136 103 0.125 65 0.079 0.662 0.338 18880 12552 6600 18678 0 0 0 0 0 0 0 0 0 0 0 0 0 77 0 -------------------------------------------------------------------------------- /datasets/Dornburg_2012/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Dornburg A, Moore JA, Webster R, Warren DL, Brandley MC, Iglesias TL, Wainwright PC, Near TJ. Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei: Beryciformes: Holocentridae): Reconciling more than 100 years of taxonomic confusion. Molecular phylogenetics and Evolution. 2012 Nov 30;65(2):727-38." 3 | year: 2013 4 | DOI: dx.doi.org/10.1016/j.ympev.2012.07.020 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.3t19n 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 44 12 | nchar: 5919 13 | datatype: nucleotide 14 | partitions: 21 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 144.4 mya 25 | study root age: NA 26 | study clade: 27 | latin: "Teleostei: Beryciformes: Holocentridae" 28 | english: "Squirrel Fishes" 29 | taxon ID: 47697 30 | notes: NA 31 | -------------------------------------------------------------------------------- /datasets/Dornburg_2012/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex Beryx_decadactylus 5919 504 8.515 0.465 0.535 1314 1462 1434 1204 0 0 0 1 0 0 0 0 0 0 0 0 0 504 0 3 | alignment.nex Corniger_spinosus 5919 5268 89.002 0.527 0.473 157 191 117 186 0 0 0 0 0 0 0 0 0 0 0 0 0 5268 0 4 | alignment.nex Holocentrus_adscensionis 5919 884 14.935 0.48 0.52 1250 1345 1273 1167 0 0 0 0 0 0 0 0 0 0 0 2 0 880 2 5 | alignment.nex Holocentrus_rufus 5919 360 6.082 0.48 0.52 1368 1465 1426 1300 0 0 0 0 0 0 0 0 0 0 0 5 0 353 2 6 | alignment.nex Myripristis_adusta 5919 1438 24.295 0.484 0.516 1089 1208 1106 1078 0 0 0 0 0 0 0 0 0 0 0 0 0 1438 0 7 | alignment.nex Myripristis_amaena 5919 854 14.428 0.48 0.52 1241 1357 1275 1192 0 0 0 0 0 0 0 0 0 0 0 1 0 852 1 8 | alignment.nex Myripristis_berndti 5919 1480 25.004 0.481 0.519 1075 1207 1099 1058 0 0 0 0 0 0 0 0 0 0 0 0 0 1480 0 9 | alignment.nex Myripristis_botche 5919 789 13.33 0.482 0.518 1244 1354 1303 1229 0 0 0 0 0 0 0 0 0 0 0 2 0 787 0 10 | alignment.nex Myripristis_chryseres 5919 1493 25.224 0.479 0.521 1069 1208 1097 1052 0 0 0 0 0 0 0 0 0 0 0 0 0 1491 2 11 | alignment.nex Myripristis_hexagona 5919 1486 25.106 0.48 0.52 1077 1207 1099 1050 0 0 0 0 0 0 0 0 0 0 0 1 0 1485 0 12 | alignment.nex Myripristis_jacobus 5919 695 11.742 0.484 0.516 1281 1379 1318 1246 0 0 0 0 0 0 0 0 0 0 0 3 0 692 0 13 | alignment.nex Myripristis_kuntee 5919 1252 21.152 0.477 0.523 1123 1264 1175 1105 0 0 0 0 0 0 0 0 0 0 0 4 0 1248 0 14 | alignment.nex Myripristis_leioganthus 5919 736 12.435 0.481 0.519 1237 1358 1333 1255 0 0 0 0 0 0 0 0 0 0 0 3 0 733 0 15 | alignment.nex Myripristis_murdjan 5919 157 2.652 0.481 0.519 1399 1505 1482 1372 0 1 0 3 0 0 0 0 0 0 0 0 0 157 0 16 | alignment.nex Myripristis_pralinia 5919 1227 20.73 0.478 0.522 1140 1267 1181 1104 0 0 0 0 0 0 0 0 0 0 0 2 0 1225 0 17 | alignment.nex Myripristis_randalli 5919 845 14.276 0.477 0.523 1238 1373 1281 1182 0 0 0 0 0 0 0 0 0 0 0 2 0 841 2 18 | alignment.nex Myripristis_violacea 5919 103 1.74 0.478 0.522 1403 1534 1501 1375 0 0 1 2 0 0 0 0 0 0 0 0 0 103 0 19 | alignment.nex Myripristis_vittata 5919 974 16.455 0.477 0.523 1200 1341 1245 1159 0 0 0 0 0 0 0 0 0 0 0 2 0 971 1 20 | alignment.nex Neoniphon_argenteus 5919 1800 30.411 0.481 0.519 1005 1078 1058 978 0 0 0 0 0 0 0 0 0 0 0 0 0 1800 0 21 | alignment.nex Neoniphon_marianus 5919 1326 22.402 0.476 0.524 1121 1206 1199 1067 0 0 0 0 0 0 0 0 0 0 0 15 0 1311 0 22 | alignment.nex Neoniphon_opercularis 5919 586 9.9 0.483 0.517 1332 1365 1392 1244 0 0 0 0 0 0 0 0 0 0 0 8 0 578 0 23 | alignment.nex Neoniphon_sammara 5919 1034 17.469 0.486 0.514 1204 1281 1232 1168 0 0 0 0 0 0 0 0 0 0 0 0 0 1034 0 24 | alignment.nex Ostichthys_trachypoma 5919 1934 32.674 0.47 0.53 951 1099 1015 920 0 0 0 0 0 0 0 0 0 0 0 0 0 1930 4 25 | alignment.nex Percopsis_omiscomaycus 5919 140 2.365 0.437 0.563 1301 1645 1606 1226 0 0 1 0 0 0 0 0 0 0 0 0 0 140 0 26 | alignment.nex Plectrypops_lima 5919 875 14.783 0.473 0.527 1229 1365 1291 1159 0 0 0 0 0 0 0 0 0 0 0 0 0 868 7 27 | alignment.nex Plectrypops_retrospinus 5919 906 15.307 0.473 0.527 1225 1381 1263 1144 0 0 0 0 0 0 0 0 0 0 0 1 0 899 6 28 | alignment.nex Sargocentron_caudimaculatum 5919 1116 18.855 0.478 0.522 1158 1279 1226 1140 0 0 0 0 0 0 0 0 0 0 0 2 0 1102 12 29 | alignment.nex Sargocentron_cornutum 5919 535 9.039 0.473 0.527 1287 1420 1418 1256 0 1 2 0 0 0 0 0 0 0 0 7 0 528 0 30 | alignment.nex Sargocentron_coruscum 5919 1107 18.702 0.483 0.517 1180 1268 1221 1143 0 0 0 0 0 0 0 0 0 0 0 4 0 1101 2 31 | alignment.nex Sargocentron_diadema 5919 2205 37.253 0.475 0.525 908 1000 949 857 0 0 0 0 0 0 0 0 0 0 0 0 0 2202 3 32 | alignment.nex Sargocentron_inaequalis 5919 686 11.59 0.485 0.515 1311 1351 1345 1226 0 0 0 0 0 0 0 0 0 0 0 4 0 682 0 33 | alignment.nex Sargocentron_ittodai 5919 1829 30.9 0.481 0.519 1002 1120 1001 967 0 0 0 0 0 0 0 0 0 0 0 6 0 1823 0 34 | alignment.nex Sargocentron_melanospilos 5919 963 16.27 0.48 0.52 1187 1318 1260 1191 0 0 0 0 0 0 0 0 0 0 0 0 0 963 0 35 | alignment.nex Sargocentron_microstoma 5919 1148 19.395 0.478 0.522 1154 1264 1226 1127 0 0 0 0 0 0 0 0 0 0 0 1 0 1147 0 36 | alignment.nex Sargocentron_praslin 5919 409 6.91 0.475 0.525 1326 1455 1439 1290 0 0 0 0 0 0 0 0 0 0 0 10 0 399 0 37 | alignment.nex Sargocentron_punctassimum 5919 1550 26.187 0.484 0.516 1085 1167 1087 1030 0 0 0 0 0 0 0 0 0 0 0 0 0 1550 0 38 | alignment.nex Sargocentron_rubrum 5919 1171 19.784 0.468 0.532 1142 1258 1267 1081 0 0 0 0 0 0 0 0 0 0 0 11 0 1160 0 39 | alignment.nex Sargocentron_seychellense 5919 462 7.805 0.472 0.528 1312 1453 1429 1263 0 0 0 0 0 0 0 0 0 0 0 2 0 457 3 40 | alignment.nex Sargocentron_spiniferum 5919 1029 17.385 0.479 0.521 1183 1297 1253 1157 0 0 0 0 0 0 0 0 0 0 0 6 0 1023 0 41 | alignment.nex Sargocentron_suborbitalis 5919 1431 24.176 0.487 0.513 1088 1183 1120 1097 0 0 0 0 0 0 0 0 0 0 0 8 0 1423 0 42 | alignment.nex Sargocentron_tiere 5919 536 9.056 0.474 0.526 1315 1421 1408 1239 0 0 0 0 0 0 0 0 0 0 0 32 0 503 1 43 | alignment.nex Sargocentron_tiereoides 5919 5335 90.133 0.56 0.44 150 157 100 177 0 0 0 0 0 0 0 0 0 0 0 0 0 5335 0 44 | alignment.nex Sargocentron_vexillarium 5919 964 16.287 0.474 0.526 1208 1295 1310 1139 0 0 1 2 0 0 0 0 0 0 0 5 0 959 0 45 | alignment.nex Sargocentron_xantherythrum 5919 5269 89.018 0.549 0.451 168 176 117 189 0 0 0 0 0 0 0 0 0 0 0 0 0 5269 0 -------------------------------------------------------------------------------- /datasets/Dornburg_2012/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 44 5919 260436 56891 21.845 1560 0.264 896 0.151 0.482 0.518 49437 54327 51977 47789 0 2 5 8 0 0 0 0 0 0 0 149 0 56694 48 -------------------------------------------------------------------------------- /datasets/Faircloth_2013/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Faircloth BC, Sorenson L, Santini F, Alfaro ME (2013) A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). PLoS ONE 8(6): e65923" 3 | year: 2013 4 | DOI: dx.doi.org/10.1371/journal.pone.0065923 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.j015n 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 27 12 | nchar: 149366 13 | datatype: nucleotide 14 | partitions: 491 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 386.7 mya 25 | study root age: NA 26 | study clade: 27 | latin: Actinopterygii 28 | english: Ray-finned fishes 29 | taxon ID: 7898 30 | notes: The individual UCEs in the file "fish-nexus-files-with-gaps-from-uce-alignment.tar.gz" were concatenated into a single .nex file 31 | -------------------------------------------------------------------------------- /datasets/Faircloth_2013/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex acanthurus_japonicus 149366 36509 24.443 0.557 0.443 31274 25151 24829 31603 0 0 0 0 0 0 0 0 0 0 0 0 0 36509 0 3 | alignment.nex acipenser_fulvescens 149366 112535 75.342 0.58 0.42 10680 7863 7597 10691 0 0 0 0 0 0 0 0 0 0 0 0 0 112535 0 4 | alignment.nex amia_calva 149366 63898 42.779 0.582 0.418 24692 18030 17700 25046 0 0 0 0 0 0 0 0 0 0 0 0 0 63898 0 5 | alignment.nex anchoa_compressa 149366 82715 55.377 0.548 0.452 18093 15232 14875 18451 0 0 0 0 0 0 0 0 0 0 0 0 0 82715 0 6 | alignment.nex antennarius_striatus 149366 44026 29.475 0.565 0.435 29512 23370 22402 30056 0 0 0 0 0 0 0 0 0 0 0 0 0 44026 0 7 | alignment.nex astyanax_fasciatus 149366 66913 44.798 0.546 0.454 22505 18841 18611 22496 0 0 0 0 0 0 0 0 0 0 0 0 0 66913 0 8 | alignment.nex danio_rerio 149366 64692 43.311 0.552 0.448 23130 19019 18908 23617 0 0 0 0 0 0 0 0 0 0 0 0 0 64692 0 9 | alignment.nex diaphus_theta 149366 53086 35.541 0.559 0.441 26499 21645 20805 27331 0 0 0 0 0 0 0 0 0 0 0 0 0 53086 0 10 | alignment.nex gadus_morhua 149366 51130 34.231 0.535 0.465 26089 23101 22595 26451 0 0 0 0 0 0 0 0 0 0 0 0 0 51130 0 11 | alignment.nex gasterosteus_aculeatus 149366 23471 15.714 0.544 0.456 34122 28879 28527 34367 0 0 0 0 0 0 0 0 0 0 0 0 0 23471 0 12 | alignment.nex haplochromis_burtoni 149366 24935 16.694 0.554 0.446 34216 27934 27550 34731 0 0 0 0 0 0 0 0 0 0 0 0 0 24935 0 13 | alignment.nex lampris_guttatus 149366 48138 32.228 0.556 0.444 27991 22819 22111 28307 0 0 0 0 0 0 0 0 0 0 0 0 0 48138 0 14 | alignment.nex lepisosteus_oculatus 149366 42187 28.244 0.581 0.419 31032 22588 22268 31291 0 0 0 0 0 0 0 0 0 0 0 0 0 42187 0 15 | alignment.nex megalops_sp 149366 95191 63.73 0.57 0.43 15247 11855 11460 15613 0 0 0 0 0 0 0 0 0 0 0 0 0 95191 0 16 | alignment.nex neolamprologus_brichardi 149366 25696 17.203 0.553 0.447 33972 27796 27521 34381 0 0 0 0 0 0 0 0 0 0 0 0 0 25696 0 17 | alignment.nex oreochromis_niloticus 149366 23948 16.033 0.554 0.446 34482 28133 27804 34999 0 0 0 0 0 0 0 0 0 0 0 0 0 23948 0 18 | alignment.nex oryzias_latipes 149366 25632 17.161 0.554 0.446 34009 27787 27394 34544 0 0 0 0 0 0 0 0 0 0 0 0 0 25632 0 19 | alignment.nex osteoglossum_bicirrhosum 149366 89355 59.823 0.548 0.452 16353 13739 13406 16513 0 0 0 0 0 0 0 0 0 0 0 0 0 89355 0 20 | alignment.nex pantodon_buchholzi 149366 86912 58.187 0.552 0.448 17200 14166 13843 17245 0 0 0 0 0 0 0 0 0 0 0 0 0 86912 0 21 | alignment.nex polypterus_senegalus 149366 75780 50.734 0.586 0.414 21721 15515 14986 21364 0 0 0 0 0 0 0 0 0 0 0 0 0 75780 0 22 | alignment.nex pundamilia_nyererei 149366 24491 16.397 0.554 0.446 34337 28075 27629 34834 0 0 0 0 0 0 0 0 0 0 0 0 0 24491 0 23 | alignment.nex salvelinus_fontinalis 149366 115455 77.297 0.557 0.443 9368 7685 7337 9521 0 0 0 0 0 0 0 0 0 0 0 0 0 115455 0 24 | alignment.nex strophidon_sathete 149366 84478 56.558 0.568 0.432 18212 14209 13855 18612 0 0 0 0 0 0 0 0 0 0 0 0 0 84478 0 25 | alignment.nex taenianotus_triacanthus 149366 38827 25.995 0.554 0.446 30447 24881 24468 30743 0 0 0 0 0 0 0 0 0 0 0 0 0 38827 0 26 | alignment.nex takifugu_rupribes 149366 22954 15.368 0.548 0.452 34452 28802 28371 34787 0 0 0 0 0 0 0 0 0 0 0 0 0 22954 0 27 | alignment.nex tetraodon_nigroviridis 149366 23037 15.423 0.549 0.451 34555 28759 28206 34809 0 0 0 0 0 0 0 0 0 0 0 0 0 23037 0 28 | alignment.nex umbra_limi 149366 55658 37.263 0.566 0.434 26245 20675 20035 26753 0 0 0 0 0 0 0 0 0 0 0 0 0 55658 0 -------------------------------------------------------------------------------- /datasets/Faircloth_2013/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 27 149366 4032882 1501649 37.235 57607 0.386 29564 0.198 0.558 0.442 700435 566549 555093 709156 0 0 0 0 0 0 0 0 0 0 0 0 0 1501649 0 -------------------------------------------------------------------------------- /datasets/Fong_2012/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Fong JJ, Brown JM, Fujita MK, Boussau B. A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia. PLoS One. 2012 Nov 7;7(11):e48990." 3 | year: 2012 4 | DOI: dx.doi.org/10.1371/journal.pone.0048990 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.25j6h 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 110 12 | nchar: 25919 13 | datatype: nucleotide 14 | partitions: 168 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: Vertebrata 28 | english: vertebrates 29 | taxon ID: 7742 30 | notes: This is the SlowGenes dataset from Dryad 31 | 32 | -------------------------------------------------------------------------------- /datasets/Fong_2012/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 110 25919 2851090 1594272 55.918 12133 0.468 9712 0.375 0.532 0.468 374260 266090 311529 302822 307 327 442 481 240 319 1 0 0 0 0 0 0 25623 1568649 -------------------------------------------------------------------------------- /datasets/Horn_2014/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Horn JW, Xi Z, Riina R, Peirson JA, Yang Y, Dorsey BL, Berry PE, Davis CC, Wurdack KJ (2014) Evolutionary bursts in Euphorbia (Euphorbiaceae) are linked with photosynthetic pathway. Evolution 68(12): 3485-3504." 3 | year: 2014 4 | DOI: dx.doi.org/10.1111/evo.12534 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.sb1j1 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 197 12 | nchar: 11587 13 | datatype: nucleotide 14 | partitions: 28 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: yes 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 61.8 mya 25 | study root age: 47.8 mya 26 | study clade: 27 | latin: Euphorbia 28 | english: spurge 29 | taxon ID: 3990 30 | notes: NA 31 | -------------------------------------------------------------------------------- /datasets/Horn_2014/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 197 11587 2282639 343789 15.061 5177 0.447 3525 0.304 0.593 0.407 594303 366701 421382 555468 62 74 302 381 73 104 0 0 0 0 0 1731 0 33193 308865 -------------------------------------------------------------------------------- /datasets/Irisarri_2017/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Irisarri I, Baurain D, Brinkmann H, Delsuc F, Sire J, Kupfer A, Petersen J, Jarek M, Meyer A, Vences M, Philippe H (2017) Phylotranscriptomic consolidation of the jawed vertebrate timetree. Nature Ecology & Evolution 1(9): 1370-1378. https://doi.org/10.1038/s41559-017-0240-5" 3 | year: 2017 4 | DOI: dx.doi.org/10.1038/s41559-017-0240-5 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.r2n70 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 100 12 | nchar: 1964439 13 | datatype: protein 14 | partitions: 4593 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 473 mya 25 | study root age: 458 mya 26 | study clade: 27 | latin: Gnathostomata 28 | english: Jawed vertebrates 29 | taxon ID: 7776 30 | notes: This is the 0DP-4593_single_genes dataset, which was used to create the main figure in the paper. Charsets are named according to the original files, but with non-alphanumeric characters removed. 31 | -------------------------------------------------------------------------------- /datasets/Irisarri_2017/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 100 1964439 196443900 62866306 32.002 1285039 0.654 1069208 0.544 8561703 2853642 6902798 9583997 5488652 7696666 3436178 6955048 8865754 13667831 3181864 5362169 6474527 6101470 7169288 9950678 6863596 8534042 1674636 4253055 0 0 0 5484 0 0 0 62860822 -------------------------------------------------------------------------------- /datasets/Jarvis_2015/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Erich D Jarvis, Siavash Mirarab, Andre J Aberer, Bo Li, Peter Houde, Cai Li, Simon Y W Ho, Brant C Faircloth, Benoit Nabholz, Jason T Howard, Alexander Suh, Claudia C Weber, Rute R da Fonseca, Alonzo Alfaro-Núñez, Nitish Narula, Liang Liu, Dave Burt, Hans Ellegren, Scott V Edwards, Alexandros Stamatakis, David P Mindell, Joel Cracraft, Edward L Braun, Tandy Warnow, Wang Jun, M Thomas Pius Gilbert, Guojie Zhang, The Avian Phylogenomics Consortium, Phylogenomic analyses data of the avian phylogenomics project, GigaScience, Volume 4, Issue 1, December 2015, s13742–014–0038–1" 3 | year: 2015 4 | DOI: dx.doi.org/10.1186/s13742-014-0038-1 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5524/101041 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 52 12 | nchar: 4519041 13 | datatype: protein 14 | partitions: 8295 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 111 mya 25 | study root age: 102 mya 26 | study clade: 27 | latin: Aves 28 | english: birds 29 | taxon ID: 8782 30 | notes: This dataset is 8295 exons in amino acids from this download 'ftp://parrot.genomics.cn/gigadb/pub/10.5524/101001_102000/101041/FASTA_files_of_loci_datasets.tar.gz' and is in the following path '8295_Amino_Acids/pep-filtered-sate-alignments-original.zip'. The study root age comes from the study paired with this dataset, published in science. This study may also be worth citing when using this dataset dx.doi.org/10.1126/science.1253451 31 | -------------------------------------------------------------------------------- /datasets/Jarvis_2015/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 52 4519041 234990132 39109330 16.643 2000240 0.443 1124066 0.249 12525137 4251861 9922078 14297049 7649993 11188593 4954229 9856042 12898481 19122857 4436986 8180642 10175570 9251825 10081580 16182903 10485754 12263494 2296047 5859681 0 0 0 46129 0 0 26518464 12544737 -------------------------------------------------------------------------------- /datasets/Kawahara_2013/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Kawahara AY, Rubinoff D. Convergent evolution of morphology and habitat use in the explosive Hawaiian fancy case caterpillar radiation. Journal of evolutionary biology. 2013 Aug 1;26(8):1763-73." 3 | year: 2013 4 | DOI: dx.doi.org/10.1111/jeb.12176 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.gh895 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 70 12 | nchar: 2238 13 | datatype: nucleotide 14 | partitions: 9 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: "Hyposmocoma" 28 | english: "Hawaiian fancy cased caterpillars" 29 | taxon ID: 545366 30 | notes: Species names can be resolved using the supp info of the paper itself 31 | -------------------------------------------------------------------------------- /datasets/Kawahara_2013/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 70 2238 156660 16718 10.672 771 0.345 567 0.253 0.614 0.386 41663 27437 27063 43761 2 3 2 5 2 4 0 0 0 0 0 16718 0 0 0 -------------------------------------------------------------------------------- /datasets/Lartillot_2012/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Lartillot N, Delsuc F. Joint reconstruction of divergence times and life‐history evolution in placental mammals using a phylogenetic covariance model. Evolution. 2012 Jun 1;66(6):1773-87." 3 | year: 2012 4 | DOI: dx.doi.org/10.1111/j.1558-5646.2011.01558.x 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.tt28qk6f 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 78 12 | nchar: 15117 13 | datatype: nucleotide 14 | partitions: 51 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 105 mya 25 | study root age: 100 mya 26 | study clade: 27 | latin: "Eutheria" 28 | english: "placental mammals" 29 | taxon ID: 9347 30 | notes: NA 31 | -------------------------------------------------------------------------------- /datasets/Lartillot_2012/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 78 15117 1179126 212861 18.052 10561 0.699 9047 0.598 0.492 0.508 251575 250294 240105 224191 8 4 37 41 4 5 0 1 0 0 0 11450 0 32691 168720 -------------------------------------------------------------------------------- /datasets/Leache_2015/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Leaché, A. D., Chavez, A. S., Jones, L. N., Grummer, J. A., Gottscho, A. D., & Linkem, C. W. (2015). Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing. Genome biology and evolution, 7(3), 706-719." 3 | year: 2015 4 | DOI: dx.doi.org/10.1093/gbe/evv026 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.4vt08 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 11 12 | nchar: 358363 13 | datatype: nucleotide 14 | partitions: 583 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 50.6 mya 25 | study root age: 54 mya 26 | study clade: 27 | latin: "Phrynosomatinae" 28 | english: "Iguanian lizards" 29 | taxon ID: 6615 30 | notes: NA -------------------------------------------------------------------------------- /datasets/Leache_2015/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex callisaurus_draconoides 358363 15958 4.453 0.616 0.384 106879 65564 65978 103984 0 0 0 0 0 0 0 0 0 0 0 0 0 11167 4791 3 | alignment.nex cophosaurus_texanus 358363 32374 9.034 0.615 0.385 101647 62703 62836 98803 0 0 0 0 0 0 0 0 0 0 0 0 0 26023 6351 4 | alignment.nex gambelia_wislizenii 358363 51927 14.49 0.616 0.384 95382 58554 59049 93451 0 0 0 0 0 0 0 0 0 0 0 0 0 31090 20837 5 | alignment.nex holbrookia_maculata 358363 27292 7.616 0.615 0.385 103140 63653 63692 100586 0 0 0 0 0 0 0 0 0 0 0 0 0 21060 6232 6 | alignment.nex liolaemus_darwinii 358363 18586 5.186 0.615 0.385 105796 65471 65496 103014 0 0 0 0 0 0 0 0 0 0 0 0 0 16939 1647 7 | alignment.nex petrosaurus_thalassinus 358363 99890 27.874 0.62 0.38 81159 48935 49272 79107 0 0 0 0 0 0 0 0 0 0 0 0 0 61416 38474 8 | alignment.nex phrynosoma_sherbrookei 358363 13047 3.641 0.617 0.383 107992 65812 66338 105174 0 0 0 0 0 0 0 0 0 0 0 0 0 10624 2423 9 | alignment.nex sceloporus_occidentalis 358363 45420 12.674 0.62 0.38 98207 59174 59666 95896 0 0 0 0 0 0 0 0 0 0 0 0 0 17151 28269 10 | alignment.nex uma_notata 358363 29902 8.344 0.616 0.384 102497 62873 63338 99753 0 0 0 0 0 0 0 0 0 0 0 0 0 26894 3008 11 | alignment.nex urosaurus_ornatus 358363 22712 6.338 0.616 0.384 104761 64328 64673 101889 0 0 0 0 0 0 0 0 0 0 0 0 0 19728 2984 12 | alignment.nex uta_stansburiana 358363 42476 11.853 0.619 0.381 99069 59975 60363 96480 0 0 0 0 0 0 0 0 0 0 0 0 0 12392 30084 -------------------------------------------------------------------------------- /datasets/Leache_2015/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 11 358363 3941993 399584 10.137 40413 0.113 11850 0.033 0.617 0.383 1106529 677042 680701 1078137 0 0 0 0 0 0 0 0 0 0 0 0 0 254484 145100 -------------------------------------------------------------------------------- /datasets/Looney_2016/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Looney BP, Ryberg M, Hampe F, Sánchez-García M, Matheny PB (2016) Into and out of the tropics: global diversification patterns in a hyper-diverse clade of ectomycorrhizal fungi. Molecular Ecology 25(2): 630–647." 3 | year: 2016 4 | DOI: dx.doi.org/10.1111/mec.13506 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.gn4p4 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 1171 12 | nchar: 3927 13 | datatype: nucleotide 14 | partitions: 4 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: yes 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: 44 mya 26 | study clade: 27 | latin: Russula 28 | english: Russula 29 | taxon ID: 5402 30 | notes: There is some uncertainty about the outgroups in this dataset. The paper lists them as "Lactifluus deceptivus, Lactarius lignyotus and Multifurca zonaria", but the first outgroup does not exist in the alignment - it seems to be listed as "Lactarius deceptivus". 31 | -------------------------------------------------------------------------------- /datasets/Looney_2016/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 1171 3927 4598517 3639215 79.139 1967 0.501 1617 0.412 0.51 0.49 223115 238256 238815 257975 34 52 255 681 52 63 2 1 1 0 0 0 0 3638197 1018 -------------------------------------------------------------------------------- /datasets/McCormack_2013/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "McCormack JE, Harvey MG, Faircloth BC, Crawford NG, Glenn TC, Brumfield RT. A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS One. 2013 Jan 29;8(1):e54848." 3 | year: 2013 4 | DOI: dx.doi.org/10.1371/journal.pone.0054848 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.sd080 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 33 12 | nchar: 539526 13 | datatype: nucleotide 14 | partitions: 1541 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 82.8 mya 25 | study root age: NA 26 | study clade: 27 | latin: "Neoaves" 28 | english: "birds" 29 | taxon ID: 8782 30 | notes: Thanks to Brant Faircloth for providing additional data on the locations of the UCEs -------------------------------------------------------------------------------- /datasets/McCormack_2013/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex ardeotis_kori 539526 68166 12.634 0.632 0.368 148132 88826 84748 149654 0 0 0 0 0 0 0 0 0 0 0 0 0 68166 0 3 | alignment.nex balaeniceps_rex 539526 54594 10.119 0.633 0.367 152695 91234 86597 154406 0 0 0 0 0 0 0 0 0 0 0 0 0 54594 0 4 | alignment.nex cathartes_aura 539526 41583 7.707 0.632 0.368 156485 93837 89186 158435 0 0 0 0 0 0 0 0 0 0 0 3 0 41580 0 5 | alignment.nex colibri_coruscans 539526 82443 15.281 0.633 0.367 143683 86118 81675 145607 0 0 0 0 0 0 0 0 0 0 0 10 0 82433 0 6 | alignment.nex eudyptula_minor 539526 33156 6.145 0.631 0.369 158893 95656 91311 160510 0 0 0 0 0 0 0 0 0 0 0 10 0 33146 0 7 | alignment.nex eurypyga_helias 539526 40356 7.48 0.631 0.369 156764 94320 89983 158103 0 0 0 0 0 0 0 0 0 0 0 0 0 40356 0 8 | alignment.nex gallus_gallus 539526 13401 2.484 0.629 0.371 164470 99896 95221 166538 0 0 0 0 0 0 0 0 0 0 0 13 0 13388 0 9 | alignment.nex gampsonyx_swainsonii 539526 83509 15.478 0.633 0.367 143021 86319 81240 145437 0 0 0 0 0 0 0 0 0 0 0 0 0 83509 0 10 | alignment.nex gavia_immer 539526 61782 11.451 0.631 0.369 149748 90381 85706 151909 0 0 0 0 0 0 0 0 0 0 0 0 0 61782 0 11 | alignment.nex megalaima_virens 539526 179052 33.187 0.629 0.371 112297 69073 64767 114337 0 0 0 0 0 0 0 0 0 0 0 0 0 179052 0 12 | alignment.nex micrastur_semitorquatus 539526 338948 62.823 0.629 0.371 62336 38879 35525 63838 0 0 0 0 0 0 0 0 0 0 0 0 0 338948 0 13 | alignment.nex momotus_momota 539526 56762 10.521 0.629 0.371 151072 91952 87369 152371 0 0 0 0 0 0 0 0 0 0 0 0 0 56762 0 14 | alignment.nex nyctibius_grandis 539526 85708 15.886 0.633 0.367 143046 85210 81448 144114 0 0 0 0 0 0 0 0 0 0 0 9 0 85699 0 15 | alignment.nex oceanites_oceanicus 539526 32189 5.966 0.631 0.369 159155 95829 91300 161053 0 0 0 0 0 0 0 0 0 0 0 10 0 32179 0 16 | alignment.nex opisthocomus_hoazin 539526 190841 35.372 0.627 0.373 108570 67201 62913 110001 0 0 0 0 0 0 0 0 0 0 0 0 0 190841 0 17 | alignment.nex phaethon_rubicauda 539526 66252 12.28 0.634 0.366 149245 88788 84545 150696 0 0 0 0 0 0 0 0 0 0 0 0 0 66252 0 18 | alignment.nex phalacrocorax_carbo 539526 70657 13.096 0.632 0.368 147407 88573 83956 148933 0 0 0 0 0 0 0 0 0 0 0 0 0 70657 0 19 | alignment.nex phegornis_mitchelli 539526 77577 14.379 0.631 0.369 145084 87396 83107 146362 0 0 0 0 0 0 0 0 0 0 0 0 0 77577 0 20 | alignment.nex phoenicopterus_chilensis 539526 76440 14.168 0.632 0.368 145956 87445 82876 146809 0 0 0 0 0 0 0 0 0 0 0 0 0 76440 0 21 | alignment.nex pitta_guajana 539526 59107 10.955 0.631 0.369 150875 90690 86482 152372 0 0 0 0 0 0 0 0 0 0 0 0 0 59107 0 22 | alignment.nex podiceps_auritus 539526 110758 20.529 0.636 0.364 135460 80174 75967 137167 0 0 0 0 0 0 0 0 0 0 0 0 0 110758 0 23 | alignment.nex psittacula_alexandri 539526 65902 12.215 0.632 0.368 149189 89147 84929 150359 0 0 0 0 0 0 0 0 0 0 0 3 0 65899 0 24 | alignment.nex psophia_crepitans 539526 69877 12.952 0.631 0.369 147175 89033 84420 149021 0 0 0 0 0 0 0 0 0 0 0 0 0 69877 0 25 | alignment.nex pterocles 539526 194825 36.11 0.638 0.362 109559 63985 60639 110518 0 0 0 0 0 0 0 0 0 0 0 0 0 194825 0 26 | alignment.nex rhinopomastus_cyanomelas 539526 97735 18.115 0.619 0.381 135922 86352 81826 137691 0 0 0 0 0 0 0 0 0 0 0 0 0 97735 0 27 | alignment.nex scopus_umbretta 539526 33034 6.123 0.631 0.369 158683 95823 91282 160704 0 0 0 0 0 0 0 0 0 0 0 0 0 33034 0 28 | alignment.nex tauraco_erythrolophus 539526 50630 9.384 0.63 0.37 153200 92575 88110 155011 0 0 0 0 0 0 0 0 0 0 0 0 0 50630 0 29 | alignment.nex treron_vernans 539526 107000 19.832 0.633 0.367 136177 81362 77324 137663 0 0 0 0 0 0 0 0 0 0 0 0 0 107000 0 30 | alignment.nex trogon_personata 539526 223637 41.451 0.624 0.376 97667 61453 57268 99501 0 0 0 0 0 0 0 0 0 0 0 0 0 223637 0 31 | alignment.nex tyto_alba 539526 93905 17.405 0.632 0.368 140175 84215 79668 141563 0 0 0 0 0 0 0 0 0 0 0 0 0 93905 0 32 | alignment.nex urocolius_indicus 539526 67415 12.495 0.633 0.367 148595 88754 84649 150113 0 0 0 0 0 0 0 0 0 0 0 0 0 67415 0 33 | alignment.nex vidua_macroura 539526 328506 60.888 0.609 0.391 63115 43266 39207 65432 0 0 0 0 0 0 0 0 0 0 0 0 0 328506 0 34 | alignment.nex zanclostomus_javanicus 539526 76761 14.227 0.624 0.376 143383 89410 84487 145485 0 0 0 0 0 0 0 0 0 0 0 0 0 76761 0 -------------------------------------------------------------------------------- /datasets/McCormack_2013/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 33 539526 17804358 3232508 18.156 88014 0.163 24703 0.046 0.63 0.37 4567234 2763172 2619731 4621713 0 0 0 0 0 0 0 0 0 0 0 58 0 3232450 0 -------------------------------------------------------------------------------- /datasets/Meiklejohn_2016/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Meiklejohn, K. A., Faircloth, B. C., Glenn, T. C., Kimball, R. T., & Braun, E. L. (2016). Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods. Systematic biology, syw014." 3 | year: 2016 4 | DOI: dx.doi.org/10.1093/sysbio/syw014 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.p1m52 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 18 12 | nchar: 614159 13 | datatype: nucleotide 14 | partitions: 1501 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 48.2 mya 25 | study root age: NA 26 | study clade: 27 | latin: Phasianidae 28 | english: Gallopheasants 29 | taxon ID: 9005 30 | notes: Thanks to Brant Faircloth for providing additional data 31 | -------------------------------------------------------------------------------- /datasets/Meiklejohn_2016/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex alectoris_rufa 614159 121228 19.739 0.571 0.429 139166 106383 105201 142172 0 0 5 1 2 1 0 0 0 0 0 0 0 121228 0 3 | alignment.nex catreus_wallichi 614159 32723 5.328 0.574 0.426 165462 124430 123002 168539 0 1 1 1 0 0 0 0 0 0 0 0 0 32723 0 4 | alignment.nex chrysolophus_pictus 614159 24824 4.042 0.575 0.425 167667 126236 124506 170901 1 0 12 8 3 1 0 0 0 0 0 0 0 24824 0 5 | alignment.nex crossoptilon_crossoptilon 614159 43926 7.152 0.575 0.425 162424 121925 120328 165542 0 0 5 6 3 0 0 0 0 0 0 0 0 43926 0 6 | alignment.nex cyrtonyx_montezumae 614159 28755 4.682 0.574 0.426 166516 125611 123730 169535 2 1 5 2 1 1 0 0 0 0 0 0 0 28755 0 7 | alignment.nex galgal4 614159 4642 0.756 0.574 0.426 173424 130720 129003 176358 0 1 4 7 0 0 0 0 0 0 0 0 0 4642 0 8 | alignment.nex lophophorus_impejanus 614159 20227 3.293 0.576 0.424 169425 126788 125182 172514 1 1 9 10 1 1 0 0 0 0 0 0 0 20227 0 9 | alignment.nex lophura_inornata 614159 39561 6.441 0.574 0.426 163182 123278 121713 166391 1 1 12 16 2 2 0 0 0 0 0 0 0 39561 0 10 | alignment.nex lophura_nycthemera 614159 22069 3.593 0.576 0.424 168842 126575 124754 171898 2 0 9 7 2 1 0 0 0 0 0 0 0 22069 0 11 | alignment.nex lophura_swinhoii 614159 43761 7.125 0.576 0.424 162723 121587 120260 165826 0 0 1 1 0 0 0 0 0 0 0 0 0 43761 0 12 | alignment.nex melgal2 614159 8553 1.393 0.576 0.424 172905 129149 127517 176022 0 1 5 3 2 2 0 0 0 0 0 0 0 8553 0 13 | alignment.nex pavo_cristatus 614159 18303 2.98 0.573 0.427 169177 128119 126415 172143 0 0 0 1 0 1 0 0 0 0 0 0 0 18303 0 14 | alignment.nex perdix 614159 29502 4.804 0.575 0.425 166336 125112 123611 169594 0 0 1 3 0 0 0 0 0 0 0 0 0 29502 0 15 | alignment.nex phasianus_colchicus 614159 86706 14.118 0.572 0.428 149262 113946 111907 152313 1 0 10 11 2 1 0 0 0 0 0 0 0 86706 0 16 | alignment.nex rollulus_rouloul 614159 64548 10.51 0.572 0.428 155590 118406 116766 158822 2 5 10 9 1 0 0 0 0 0 0 0 0 64548 0 17 | alignment.nex syrmaticus_ellioti 614159 131245 21.37 0.573 0.427 136818 103874 102310 139893 0 0 9 10 0 0 0 0 0 0 0 1 0 131244 0 18 | alignment.nex syrmaticus_reevesii 614159 115811 18.857 0.573 0.427 141263 107210 105409 144460 0 0 2 2 1 0 0 0 1 0 0 0 0 115811 0 19 | alignment.nex tragopan_blythii 614159 72589 11.819 0.575 0.425 154188 116094 113860 157406 2 0 10 6 3 1 0 0 0 0 0 0 0 72589 0 -------------------------------------------------------------------------------- /datasets/Meiklejohn_2016/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 18 614159 11054862 908973 8.222 44898 0.073 12149 0.02 0.574 0.426 2884370 2175443 2145474 2940329 12 11 110 104 23 12 0 0 1 0 0 1 0 908972 0 -------------------------------------------------------------------------------- /datasets/Misof_2014/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Misof B, Liu S, Meusemann K, Peters RS, Donath A, Mayer C, Frandsen PB, Ware J, Flouri T, Beutel RG, Niehuis O. Phylogenomics resolves the timing and pattern of insect evolution. Science. 2014 Nov 7;346(6210):763-7." 3 | year: 2014 4 | DOI: dx.doi.org/10.1126/science.1257570 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.3c0f1 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 144 12 | nchar: 595033 13 | datatype: protein 14 | partitions: 2868 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 495.1 mya 25 | study root age: 479 mya 26 | study clade: 27 | latin: "Insecta" 28 | english: "insects" 29 | taxon ID: 50557 30 | notes: This is the largest dataset in the supplementary files, specifically, it is supermatrix A in supplementary archive 8. The partitions are from the file supermatrix_A.domains_partitions 31 | -------------------------------------------------------------------------------- /datasets/Misof_2014/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 144 595033 85684752 30989469 36.167 525304 0.883 453730 0.763 3557375 1127218 3026979 3804764 2299645 2991216 1399476 3212160 3707543 5654915 1332974 2314975 2348716 2269214 3105856 3544039 2804000 3639571 706362 1848285 0 0 0 26113167 0 0 4876302 0 -------------------------------------------------------------------------------- /datasets/Moyle_2016/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Moyle RG, Oliveros CH, Andersen MJ, Hosner PA, Benz BW, Manthey JD, Travers SL, Brown RM, Faircloth BC. Tectonic collision and uplift of Wallacea triggered the global songbird radiation. Nature Communications. 2016 Aug 30;7." 3 | year: 2016 4 | DOI: dx.doi.org/10.1038/ncomms12709 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.nf01p 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 106 12 | nchar: 375172 13 | datatype: nucleotide 14 | partitions: 515 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 53.8 mya 25 | study root age: 32 mya 26 | study clade: 27 | latin: "Oscines" 28 | english: "songbirds" 29 | taxon ID: 6615 30 | notes: additional information on UCE boundaries was kindly provided by Rob Moyle -------------------------------------------------------------------------------- /datasets/Moyle_2016/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 106 375172 39768232 2592269 6.518 139441 0.372 78546 0.209 0.6 0.4 11035989 7496648 7364336 11278990 0 0 0 0 0 0 0 0 0 0 0 0 0 78633 2513636 -------------------------------------------------------------------------------- /datasets/Murray_2013/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Murray EA, Carmichael AE, Heraty JM. Ancient host shifts followed by host conservatism in a group of ant parasitoids. Proceedings of the Royal Society of London B: Biological Sciences. 2013 May 22;280(1759):20130495." 3 | year: 2013 4 | DOI: dx.doi.org/10.1098/rspb.2013.0495 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.qn57t 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 237 12 | nchar: 3111 13 | datatype: nucleotide 14 | partitions: 9 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: "Eucharitidae" 28 | english: "eucharitid wasps" 29 | taxon ID: 216140 30 | notes: NA -------------------------------------------------------------------------------- /datasets/Murray_2013/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 237 3111 737307 281539 38.185 1183 0.38 948 0.305 0.555 0.445 119648 88762 111457 135808 9 10 20 28 6 19 0 0 0 1 0 133 0 36959 244447 -------------------------------------------------------------------------------- /datasets/Near_2013/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Near TJ, Dornburg A, Eytan RI, Keck BP, Smith WL, Kuhn KL, Moore JA, Price SA, Burbrink FT, Friedman M, Wainwright PC. Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes. Proceedings of the National Academy of Sciences. 2013 Jul 30;110(31):12738-43." 3 | year: 2013 4 | DOI: dx.doi.org/10.1073/pnas.1304661110 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.d3mb4 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 608 12 | nchar: 8577 13 | datatype: nucleotide 14 | partitions: 30 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: "Acanthomorpha" 28 | english: "spiny-rayed fishes" 29 | taxon ID: 123368 30 | notes: "There were a few issues with capitalisations in the species names, which I fixed" -------------------------------------------------------------------------------- /datasets/Near_2013/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 608 8577 5214816 1091376 20.928 5645 0.658 4780 0.557 0.453 0.547 999539 1145402 1108523 867952 111 141 586 946 137 101 0 1 0 1 0 289 0 120092 970995 -------------------------------------------------------------------------------- /datasets/Nguyen_2016a/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Nguyen AD, Gotelli NJ, Helms Cahan S (2016) The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera. BMC Evolutionary Biology 16: 15." 3 | year: 2016 4 | DOI: dx.doi.org/10.1186/s12862-015-0573-0 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.8vj6j 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 17 12 | nchar: 688 13 | datatype: protein 14 | partitions: 1 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: Hymenoptera 28 | english: sawflies, wasps, bees, and ants 29 | taxon ID: 7399 30 | notes: This is the hsc70-3 dataset from the repository. Root ages are not determined because these are trees of duplicated genes, not just taxa. 31 | -------------------------------------------------------------------------------- /datasets/Nguyen_2016a/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex A__cephalotes 688 32 4.651 47 1 55 57 23 52 8 46 62 46 13 27 26 25 27 27 44 55 2 13 0 0 0 0 0 0 32 0 3 | alignment.nex A__echinatior 688 32 4.651 47 1 55 57 23 52 8 46 62 46 13 27 26 25 27 27 44 55 2 13 0 0 0 0 0 0 32 0 4 | alignment.nex A__florea 688 4 0.581 51 2 55 60 24 54 8 46 64 50 14 30 26 25 30 29 44 54 2 16 0 0 0 0 0 0 4 0 5 | alignment.nex A__mellifera 688 30 4.36 47 1 54 57 25 52 7 45 67 48 14 27 26 23 28 27 44 51 2 13 0 0 0 0 0 0 30 0 6 | alignment.nex A__pisum 688 29 4.215 47 2 52 56 25 50 8 46 61 44 14 31 27 23 28 30 45 54 3 13 0 0 0 0 0 0 29 0 7 | alignment.nex B__impatiens 688 31 4.506 45 2 52 60 26 50 7 45 63 46 14 27 26 24 28 29 44 53 2 14 0 0 0 0 0 0 31 0 8 | alignment.nex B__mori 688 33 4.797 49 2 57 54 25 46 8 40 64 45 12 29 25 31 26 26 42 58 3 13 0 0 0 0 0 0 33 0 9 | alignment.nex B__terrestris 688 33 4.797 45 1 53 58 27 52 7 43 65 47 13 27 26 24 28 26 44 54 2 13 0 0 0 0 0 0 33 0 10 | alignment.nex C__floridanus 688 32 4.651 48 1 53 58 23 51 8 44 64 48 13 26 26 26 26 28 44 54 2 13 0 0 0 0 0 0 32 0 11 | alignment.nex C__quinquefasciatus 688 31 4.506 55 2 57 55 23 49 7 40 63 49 13 28 25 24 27 28 41 56 1 14 0 0 0 0 0 0 31 0 12 | alignment.nex D__melanogaster 688 32 4.651 50 2 55 54 24 53 9 42 64 51 10 29 26 26 26 28 37 55 2 13 0 0 0 0 0 0 32 0 13 | alignment.nex H__saltator 688 32 4.651 45 1 55 59 24 51 8 43 62 48 13 26 26 25 27 26 49 53 2 13 0 0 0 0 0 0 32 0 14 | alignment.nex L__humile 688 32 4.651 50 1 55 57 23 52 8 45 63 49 12 27 26 25 26 25 43 54 2 13 0 0 0 0 0 0 32 0 15 | alignment.nex N__vitrepennis 688 29 4.215 50 1 56 56 23 52 8 45 66 47 13 26 24 27 26 30 42 52 2 13 0 0 0 0 0 0 29 0 16 | alignment.nex P__barbatus 688 32 4.651 47 1 53 59 23 52 8 47 62 47 12 27 26 25 27 27 44 54 2 13 0 0 0 0 0 0 32 0 17 | alignment.nex S__invicta 688 32 4.651 47 1 56 56 23 52 8 46 62 46 12 27 26 25 28 27 44 55 2 13 0 0 0 0 0 0 32 0 18 | alignment.nex T__castaneum 688 117 17.006 43 3 47 42 24 44 8 37 50 39 13 26 20 21 27 22 38 55 3 9 0 0 0 0 0 0 117 0 -------------------------------------------------------------------------------- /datasets/Nguyen_2016a/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 17 688 11696 593 5.07 171 0.249 100 0.145 813 25 920 955 408 864 133 746 1064 796 218 467 433 424 462 462 733 922 36 222 0 0 0 0 0 0 593 0 -------------------------------------------------------------------------------- /datasets/Nguyen_2016b/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Nguyen AD, Gotelli NJ, Helms Cahan S (2016) The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera. BMC Evolutionary Biology 16: 15." 3 | year: 2016 4 | DOI: dx.doi.org/10.1186/s12862-015-0573-0 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.8vj6j 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 31 12 | nchar: 680 13 | datatype: protein 14 | partitions: 1 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: Hymenoptera 28 | english: sawflies, wasps, bees, and ants 29 | taxon ID: 7399 30 | notes: This is the hsc70-4 dataset from the repository. Root ages are not determined because these are trees of duplicated genes, not just taxa. 31 | -------------------------------------------------------------------------------- /datasets/Nguyen_2016b/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex A__cephalotes_h1 680 29 4.265 55 6 44 49 24 55 7 47 54 47 13 32 25 24 27 33 53 38 2 16 0 0 0 0 0 0 29 0 3 | alignment.nex A__cephalotes_h2 680 32 4.706 57 6 43 49 26 51 6 44 54 47 14 32 23 23 29 37 48 43 2 14 0 0 0 0 0 0 32 0 4 | alignment.nex A__echinatior_h1 680 29 4.265 54 6 44 49 24 55 7 47 54 47 13 32 26 24 27 34 52 38 2 16 0 0 0 0 0 0 29 0 5 | alignment.nex A__echinatior_h2 680 37 5.441 57 6 43 50 26 50 6 43 54 45 13 32 23 23 28 38 49 41 2 14 0 0 0 0 0 0 37 0 6 | alignment.nex A__florea_h1 680 30 4.412 54 6 44 49 24 57 7 44 54 46 14 32 26 24 27 31 50 42 2 17 0 0 0 0 0 0 30 0 7 | alignment.nex A__florea_h2 680 41 6.029 51 6 42 50 26 50 8 43 53 44 13 34 22 22 29 33 55 42 2 14 0 0 0 0 0 0 41 0 8 | alignment.nex A__mellifera_h1 680 30 4.412 54 6 44 49 24 57 7 44 54 46 14 32 26 24 27 31 50 42 2 17 0 0 0 0 0 0 30 0 9 | alignment.nex A__mellifera_h2 680 40 5.882 51 6 42 50 26 51 8 45 53 43 13 34 22 23 29 33 54 41 2 14 0 0 0 0 0 0 40 0 10 | alignment.nex A__pisum_h1 680 26 3.824 53 4 41 53 24 57 6 48 54 42 16 38 27 21 27 34 53 39 2 15 0 0 0 0 0 0 26 0 11 | alignment.nex A__pisum_h2 680 19 2.794 53 4 47 48 25 62 6 46 55 41 19 36 28 20 27 33 53 41 2 15 0 0 0 0 0 0 19 0 12 | alignment.nex B__impatiens 680 49 7.206 55 6 45 44 27 42 5 47 49 43 9 39 19 25 33 35 51 39 2 16 0 0 0 0 0 0 49 0 13 | alignment.nex B__impatiens_h1 680 34 5.0 53 6 44 49 24 55 7 44 54 46 13 32 25 24 27 31 51 42 2 17 0 0 0 0 0 0 34 0 14 | alignment.nex B__mori 680 31 4.559 54 4 45 51 26 55 7 45 56 44 15 33 25 25 26 31 52 38 2 15 0 0 0 0 0 0 31 0 15 | alignment.nex B__terrestris 680 49 7.206 54 6 43 44 27 41 5 49 48 43 10 42 19 25 33 36 51 37 2 16 0 0 0 0 0 0 49 0 16 | alignment.nex B__terrestris_h1 680 34 5.0 53 6 44 49 24 55 7 44 54 46 13 33 25 24 27 30 51 42 2 17 0 0 0 0 0 0 34 0 17 | alignment.nex C__floridanus_h1 680 25 3.676 56 6 43 50 24 61 7 46 54 46 14 32 25 25 27 31 51 39 2 16 0 0 0 0 0 0 25 0 18 | alignment.nex C__floridanus_h2 680 37 5.441 54 6 42 52 26 51 6 47 54 43 12 32 24 22 28 36 51 41 2 14 0 0 0 0 0 0 37 0 19 | alignment.nex C__quinquefasciatus_h1 680 34 5.0 57 5 47 47 26 52 10 43 50 45 17 34 28 22 28 35 47 39 2 12 0 0 0 0 0 0 34 0 20 | alignment.nex C__quinquefasciatus_h2 680 25 3.676 59 7 47 48 26 53 8 44 54 47 13 34 26 22 27 34 53 38 2 13 0 0 0 0 0 0 25 0 21 | alignment.nex D__melanogaster 680 29 4.265 58 5 48 47 24 53 8 43 51 50 12 32 25 23 30 31 55 40 2 14 0 0 0 0 0 0 29 0 22 | alignment.nex H__saltator_h1 680 18 2.647 55 6 44 49 24 64 7 45 55 46 14 33 27 24 28 30 52 40 3 16 0 0 0 0 0 0 18 0 23 | alignment.nex H__saltator_h2 680 42 6.176 52 6 43 51 25 47 7 46 53 42 13 31 23 24 28 39 51 41 2 14 0 0 0 0 0 0 42 0 24 | alignment.nex L__humile_h1 680 29 4.265 56 6 44 49 24 56 7 46 54 46 14 33 26 25 27 32 49 39 2 16 0 0 0 0 0 0 29 0 25 | alignment.nex L__humile_h2 680 33 4.853 56 6 44 50 26 54 7 47 53 41 13 32 24 24 28 37 52 37 2 14 0 0 0 0 0 0 33 0 26 | alignment.nex N__vitripennis_h1 680 25 3.676 57 6 44 49 24 60 7 46 52 45 14 33 25 25 27 33 48 42 2 16 0 0 0 0 0 0 25 0 27 | alignment.nex N__vitripennis_h2 680 35 5.147 53 6 44 48 24 50 5 47 51 46 12 32 26 27 28 40 50 39 2 15 0 0 0 0 0 0 35 0 28 | alignment.nex P__barbatus_h1 680 28 4.118 55 6 44 49 24 57 7 46 54 46 13 32 26 25 27 31 53 39 2 16 0 0 0 0 0 0 28 0 29 | alignment.nex P__barbatus_h2 680 33 4.853 56 6 44 49 27 53 7 47 53 43 13 32 24 23 28 36 50 40 2 14 0 0 0 0 0 0 33 0 30 | alignment.nex S__invicta_h1 680 146 21.471 46 5 37 43 17 47 5 38 45 43 10 25 19 19 22 28 41 30 1 13 0 0 0 0 0 0 146 0 31 | alignment.nex S__invicta_h2 680 36 5.294 57 6 44 50 26 49 6 46 53 43 13 31 24 23 29 40 48 40 2 14 0 0 0 0 0 0 36 0 32 | alignment.nex T__castaneum 680 31 4.559 56 5 44 51 24 54 7 46 53 44 14 35 26 24 28 34 48 38 2 16 0 0 0 0 0 0 31 0 -------------------------------------------------------------------------------- /datasets/Nguyen_2016b/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 31 680 21080 1116 5.294 233 0.343 181 0.266 1691 177 1358 1515 768 1654 210 1403 1639 1386 413 1026 759 728 863 1047 1572 1227 62 466 0 0 0 0 0 0 1116 0 -------------------------------------------------------------------------------- /datasets/Nguyen_2016c/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Nguyen AD, Gotelli NJ, Helms Cahan S (2016) The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera. BMC Evolutionary Biology 16: 15." 3 | year: 2016 4 | DOI: dx.doi.org/10.1186/s12862-015-0573-0 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.8vj6j 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 25 12 | nchar: 811 13 | datatype: protein 14 | partitions: 1 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: Hymenoptera 28 | english: sawflies, wasps, bees, and ants 29 | taxon ID: 7399 30 | notes: This is the hsp83 dataset from the repository. Root ages are not determined because these are trees of duplicated genes, not just taxa. 31 | -------------------------------------------------------------------------------- /datasets/Nguyen_2016c/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex A__cephalotes 811 42 5.179 36 8 56 95 31 34 13 49 85 68 22 30 22 26 30 51 34 48 4 27 0 0 0 0 0 0 42 0 3 | alignment.nex A__echinatior 811 87 10.727 32 8 57 94 27 32 12 46 83 61 22 30 21 22 29 46 31 44 4 23 0 0 0 0 0 0 87 0 4 | alignment.nex A__florea_h1 811 94 11.591 31 6 52 90 28 35 12 52 80 58 18 36 17 24 25 43 40 43 4 23 0 0 0 0 0 0 94 0 5 | alignment.nex A__florea_h2 811 87 10.727 35 8 57 92 27 33 12 47 81 59 21 31 24 22 29 43 30 46 4 23 0 0 0 0 0 0 87 0 6 | alignment.nex A__mellifera_h1 811 93 11.467 32 6 52 92 28 34 13 51 80 58 19 35 18 24 25 44 37 43 4 23 0 0 0 0 0 0 93 0 7 | alignment.nex A__mellifera_h2 811 87 10.727 35 8 57 91 27 34 12 47 81 59 21 31 24 22 29 43 30 46 4 23 0 0 0 0 0 0 87 0 8 | alignment.nex A__pisum_1 811 52 6.412 35 6 57 84 30 32 14 53 81 62 22 34 22 25 28 59 38 49 5 23 0 0 0 0 0 0 52 0 9 | alignment.nex A__pisum_2 811 83 10.234 37 6 60 86 25 32 12 49 79 61 20 29 22 25 28 51 33 47 4 22 0 0 0 0 0 0 83 0 10 | alignment.nex B__impatiens_h1 811 94 11.591 34 6 49 93 27 36 13 46 78 59 20 31 19 24 27 41 40 47 4 23 0 0 0 0 0 0 94 0 11 | alignment.nex B__impatiens_h2 811 86 10.604 34 8 56 94 27 33 12 48 81 59 21 29 23 22 30 45 30 46 4 23 0 0 0 0 0 0 86 0 12 | alignment.nex B__mori 811 95 11.714 38 6 54 90 23 34 13 45 75 60 20 31 22 22 31 43 31 47 4 27 0 0 0 0 0 0 95 0 13 | alignment.nex B__terrestris_h1 811 94 11.591 34 6 46 96 27 36 13 46 78 59 20 33 19 24 27 42 37 47 4 23 0 0 0 0 0 0 94 0 14 | alignment.nex B__terrestris_h2 811 86 10.604 34 8 56 94 27 33 12 48 81 59 21 29 23 22 30 45 30 46 4 23 0 0 0 0 0 0 86 0 15 | alignment.nex C__floridanus 811 89 10.974 34 8 56 92 27 33 12 45 81 61 21 30 23 22 29 45 32 44 4 23 0 0 0 0 0 0 89 0 16 | alignment.nex C__quinquefasciatus_1 811 92 11.344 45 6 61 79 28 36 10 44 77 64 22 28 19 25 25 47 28 46 4 25 0 0 0 0 0 0 92 0 17 | alignment.nex C__quinquefasciatus_2 811 95 11.714 43 6 61 80 28 37 10 44 77 62 20 28 19 24 25 48 28 47 4 25 0 0 0 0 0 0 95 0 18 | alignment.nex C__quinquefasciatus_3 811 95 11.714 44 6 61 80 28 37 10 44 77 62 20 29 19 24 25 47 28 46 4 25 0 0 0 0 0 0 95 0 19 | alignment.nex D__melanogaster 811 94 11.591 41 5 64 76 29 33 10 43 77 61 20 32 20 23 26 50 36 44 4 23 0 0 0 0 0 0 94 0 20 | alignment.nex H__saltator 811 88 10.851 36 8 59 90 27 32 12 47 81 61 21 31 24 22 29 42 30 44 4 23 0 0 0 0 0 0 88 0 21 | alignment.nex L__humile_X1 811 88 10.851 35 8 56 93 27 32 12 45 80 62 20 31 23 22 31 42 31 46 4 23 0 0 0 0 0 0 88 0 22 | alignment.nex L__humile_X2 811 88 10.851 35 8 54 95 27 32 12 46 81 61 21 31 23 22 30 42 32 44 4 23 0 0 0 0 0 0 88 0 23 | alignment.nex N__vitripennis_h1 811 116 14.303 35 7 52 89 24 33 12 41 81 59 18 31 20 19 26 42 28 49 4 25 0 0 0 0 0 0 116 0 24 | alignment.nex N__vitripennis_h2 811 180 22.195 33 8 45 69 27 30 12 44 64 56 20 29 16 23 26 42 25 39 3 20 0 0 0 0 0 0 180 0 25 | alignment.nex P__barbatus 811 89 10.974 33 8 56 92 27 33 12 48 81 61 22 31 22 22 29 44 32 42 4 23 0 0 0 0 0 0 89 0 26 | alignment.nex T__castaneum 811 90 11.097 40 6 54 89 27 37 11 47 81 59 19 32 19 23 30 44 32 44 4 23 0 0 0 0 0 0 90 0 -------------------------------------------------------------------------------- /datasets/Nguyen_2016c/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 25 811 20275 2284 11.265 296 0.365 217 0.268 901 174 1388 2215 680 843 298 1165 1981 1511 511 772 523 575 699 1131 803 1134 100 587 0 0 0 0 0 0 2284 0 -------------------------------------------------------------------------------- /datasets/Nguyen_2016d/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Nguyen AD, Gotelli NJ, Helms Cahan S (2016) The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera. BMC Evolutionary Biology 16: 15." 3 | year: 2016 4 | DOI: dx.doi.org/10.1186/s12862-015-0573-0 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.8vj6j 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 17 12 | nchar: 704 13 | datatype: protein 14 | partitions: 1 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: Hymenoptera 28 | english: sawflies, wasps, bees, and ants 29 | taxon ID: 7399 30 | notes: This is the hsc70-5 dataset from the repository. Root ages are not determined because these are trees of duplicated genes, not just taxa. 31 | -------------------------------------------------------------------------------- /datasets/Nguyen_2016d/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex A__cepahlotes 704 63 8.949 57 3 38 53 19 47 4 37 62 47 16 25 22 42 22 41 37 54 1 14 0 0 0 0 0 0 63 0 3 | alignment.nex A__echinatior 704 105 14.915 52 2 38 50 18 43 4 33 58 46 15 23 21 38 21 39 34 51 1 12 0 0 0 0 0 0 105 0 4 | alignment.nex A__florea 704 17 2.415 55 5 42 51 21 50 5 39 60 52 18 28 24 46 31 45 46 55 1 13 0 0 0 0 0 0 17 0 5 | alignment.nex A__mellifera 704 17 2.415 55 5 42 51 21 50 5 39 60 52 18 27 24 46 31 46 46 55 1 13 0 0 0 0 0 0 17 0 6 | alignment.nex A__pisum 704 24 3.409 58 3 42 46 19 51 4 41 57 53 12 29 23 50 25 50 47 57 1 12 0 0 0 0 0 0 24 0 7 | alignment.nex B__impatiens 704 17 2.415 59 4 44 50 21 49 5 40 62 51 17 26 24 47 28 41 48 55 1 15 0 0 0 0 0 0 17 0 8 | alignment.nex B__mori 704 14 1.989 61 4 44 49 20 55 6 35 52 52 18 27 24 48 35 40 48 58 1 13 0 0 0 0 0 0 14 0 9 | alignment.nex B__terrestris 704 18 2.557 59 4 44 51 21 49 5 40 62 52 15 25 24 46 28 42 48 55 1 15 0 0 0 1 0 0 17 0 10 | alignment.nex C__floridanus 704 45 6.392 62 4 40 49 20 46 5 33 61 55 15 28 23 42 26 36 43 56 1 14 0 0 0 0 0 0 45 0 11 | alignment.nex C__quinquefasciatus 704 31 4.403 63 4 44 50 18 54 7 37 61 51 17 29 20 32 27 50 41 57 1 10 0 0 0 0 0 0 31 0 12 | alignment.nex D__melanogaster 704 18 2.557 61 4 39 52 19 54 7 39 58 56 17 29 24 32 28 58 43 54 1 11 0 0 0 0 0 0 18 0 13 | alignment.nex H__saltator 704 19 2.699 58 3 42 51 21 50 5 40 64 52 17 27 23 42 26 46 43 60 1 14 0 0 0 0 0 0 19 0 14 | alignment.nex L__humile 704 18 2.557 62 4 40 55 20 47 5 37 64 53 15 29 22 45 26 42 43 61 1 15 0 0 0 0 0 0 18 0 15 | alignment.nex N__vitrepennis 704 17 2.415 66 4 39 56 23 53 5 37 61 46 18 27 25 47 30 35 45 56 1 13 0 0 0 0 0 0 17 0 16 | alignment.nex P__barbatus 704 40 5.682 64 4 37 53 22 45 5 41 65 43 16 27 22 43 25 40 42 55 1 14 0 0 0 0 0 0 40 0 17 | alignment.nex S__invicta 704 129 18.324 51 6 34 44 24 31 3 33 56 45 13 31 18 34 23 35 36 44 0 14 0 0 0 6 0 0 123 0 18 | alignment.nex T__castaneum 704 14 1.989 58 4 41 58 20 54 6 37 67 46 20 28 22 33 28 49 43 60 1 15 0 0 0 0 0 0 14 0 -------------------------------------------------------------------------------- /datasets/Nguyen_2016d/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 17 704 11968 606 5.064 331 0.47 165 0.234 1001 67 690 869 347 828 86 638 1030 852 277 465 385 713 460 735 733 943 16 227 0 0 0 7 0 0 599 0 -------------------------------------------------------------------------------- /datasets/Nguyen_2016e/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Nguyen AD, Gotelli NJ, Helms Cahan S (2016) The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera. BMC Evolutionary Biology 16: 15." 3 | year: 2016 4 | DOI: dx.doi.org/10.1186/s12862-015-0573-0 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.8vj6j 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 17 12 | nchar: 385 13 | datatype: protein 14 | partitions: 1 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: Hymenoptera 28 | english: sawflies, wasps, bees, and ants 29 | taxon ID: 7399 30 | notes: This is the hsp40 dataset from the repository. Root ages are not determined because these are trees of duplicated genes, not just taxa. 31 | -------------------------------------------------------------------------------- /datasets/Nguyen_2016e/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex A__cephalotes 385 36 9.351 25 4 25 23 22 37 8 21 35 25 5 9 22 9 21 19 19 9 1 10 0 0 0 0 0 0 36 0 3 | alignment.nex A__echinatior 385 36 9.351 27 4 25 23 22 37 8 22 35 25 5 9 22 9 21 19 17 8 1 10 0 0 0 0 0 0 36 0 4 | alignment.nex A__florea 385 48 12.468 20 3 22 21 19 38 6 21 37 24 3 11 19 12 18 20 17 15 1 10 0 0 0 0 0 0 48 0 5 | alignment.nex A__mellifera 385 48 12.468 20 3 22 21 19 39 6 21 37 24 3 11 19 12 18 19 17 15 1 10 0 0 0 0 0 0 48 0 6 | alignment.nex A__pisum 385 44 11.429 20 3 27 18 18 32 6 21 37 18 9 12 19 11 17 24 16 19 1 13 0 0 0 0 0 0 44 0 7 | alignment.nex B__impatiens 385 32 8.312 20 3 27 20 21 42 7 24 36 24 4 10 19 12 20 18 20 15 1 10 0 0 0 0 0 0 32 0 8 | alignment.nex B__mori 385 34 8.831 21 1 26 22 21 40 9 20 39 21 9 7 21 11 18 18 21 15 1 10 0 0 0 0 0 0 34 0 9 | alignment.nex B__terrestris 385 32 8.312 20 3 27 20 21 42 7 24 36 24 4 10 19 12 20 18 20 15 1 10 0 0 0 0 0 0 32 0 10 | alignment.nex C__floridanus 385 36 9.351 25 4 24 24 22 38 8 22 35 24 6 10 23 9 21 17 18 8 1 10 0 0 0 0 0 0 36 0 11 | alignment.nex C__quinquefasciatus 385 39 10.13 14 2 24 24 24 28 9 17 42 26 5 13 19 9 16 27 19 14 2 12 0 0 0 0 0 0 39 0 12 | alignment.nex D__melanogaster 385 35 9.091 21 2 27 19 26 29 8 17 40 23 7 9 20 13 18 23 18 17 1 12 0 0 0 0 0 0 35 0 13 | alignment.nex H__saltator 385 34 8.831 27 4 27 22 22 39 8 20 35 24 6 8 24 9 21 16 19 9 1 10 0 0 0 0 0 0 34 0 14 | alignment.nex L__humile 385 34 8.831 26 4 25 23 22 40 8 23 35 23 6 8 23 9 21 18 18 8 1 10 0 0 0 0 0 0 34 0 15 | alignment.nex N__vitripennis 385 149 38.701 18 2 19 16 14 38 4 11 25 14 4 3 10 6 10 8 14 11 1 8 0 0 0 0 0 0 149 0 16 | alignment.nex P__barbatus 385 23 5.974 26 6 25 26 22 38 8 20 32 27 5 12 22 9 25 22 18 10 1 8 0 0 0 0 0 0 23 0 17 | alignment.nex S__invicta 385 35 9.091 25 4 25 23 23 39 8 20 35 24 4 9 23 9 21 17 19 11 1 10 0 0 0 0 0 0 35 0 18 | alignment.nex T__castaneum 385 37 9.61 23 3 29 16 20 31 8 22 35 21 5 13 24 8 19 24 18 14 1 14 0 0 0 0 0 0 37 0 -------------------------------------------------------------------------------- /datasets/Nguyen_2016e/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 17 385 6545 732 11.184 213 0.553 133 0.345 378 55 426 361 358 627 126 346 606 391 90 164 348 169 325 327 308 213 18 177 0 0 0 0 0 0 732 0 -------------------------------------------------------------------------------- /datasets/Nguyen_2016f/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Nguyen AD, Gotelli NJ, Helms Cahan S (2016) The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera. BMC Evolutionary Biology 16: 15." 3 | year: 2016 4 | DOI: dx.doi.org/10.1186/s12862-015-0573-0 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.8vj6j 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 17 12 | nchar: 583 13 | datatype: protein 14 | partitions: 1 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: Hymenoptera 28 | english: sawflies, wasps, bees, and ants 29 | taxon ID: 7399 30 | notes: This is the hsp60 dataset from the repository. Root ages are not determined because these are trees of duplicated genes, not just taxa. 31 | -------------------------------------------------------------------------------- /datasets/Nguyen_2016f/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex A__cephalotes 583 16 2.744 59 2 39 39 9 57 2 42 48 51 15 19 18 23 25 25 32 55 1 6 0 0 0 0 0 0 16 0 3 | alignment.nex A__echinatior 583 16 2.744 59 2 39 39 9 57 2 42 47 51 15 20 18 23 25 24 33 55 1 6 0 0 0 0 0 0 16 0 4 | alignment.nex A__florea 583 13 2.23 61 3 39 38 10 58 4 36 46 53 17 24 17 19 25 26 30 57 1 6 0 0 0 0 0 0 13 0 5 | alignment.nex A__mellifera 583 13 2.23 62 3 39 38 10 58 4 37 46 53 17 24 17 19 25 26 30 55 1 6 0 0 0 0 0 0 13 0 6 | alignment.nex A__pisum 583 11 1.887 59 2 36 45 13 65 0 45 48 43 18 24 17 17 21 26 29 55 1 8 0 0 0 0 0 0 11 0 7 | alignment.nex B__impatiens 583 13 2.23 61 3 39 38 9 58 4 37 46 53 17 24 17 19 25 25 31 57 1 6 0 0 0 0 0 0 13 0 8 | alignment.nex B__mori 583 11 1.887 55 3 37 41 11 57 2 41 47 45 20 24 18 21 25 27 32 58 1 7 0 0 0 0 0 0 11 0 9 | alignment.nex B__terrestris 583 14 2.401 62 3 39 38 9 58 4 37 46 53 17 24 17 19 25 25 30 56 1 6 0 0 0 1 0 0 13 0 10 | alignment.nex C__floridanus 583 15 2.573 59 2 40 38 9 57 2 42 48 50 17 19 18 22 26 27 32 53 1 6 0 0 0 0 0 0 15 0 11 | alignment.nex C__quinquefasciatus 583 10 1.715 63 7 39 38 11 62 3 37 42 46 18 20 15 20 27 32 28 57 1 7 0 0 0 0 0 0 10 0 12 | alignment.nex D__melanogaster 583 10 1.715 58 2 38 43 9 61 1 38 46 47 21 20 17 17 28 29 33 57 1 7 0 0 0 0 0 0 10 0 13 | alignment.nex H__saltator 583 12 2.058 62 2 37 41 9 59 2 41 46 52 20 21 16 23 26 25 33 49 1 6 0 0 0 0 0 0 12 0 14 | alignment.nex L__humile 583 15 2.573 59 2 40 38 8 57 1 39 45 53 16 20 17 22 27 26 36 54 1 7 0 0 0 0 0 0 15 0 15 | alignment.nex N__vitripennis 583 11 1.887 60 2 38 39 10 59 2 36 46 49 20 22 20 21 25 28 32 56 1 6 0 0 0 0 0 0 11 0 16 | alignment.nex P__barbatus 583 14 2.401 60 2 37 40 9 59 1 42 47 49 17 22 17 22 26 25 30 56 1 7 0 0 0 0 0 0 14 0 17 | alignment.nex S__invicta 583 17 2.916 59 2 39 39 10 57 2 39 47 50 17 19 18 23 26 25 33 54 1 6 0 0 0 0 0 0 17 0 18 | alignment.nex T__castaneum 583 9 1.544 54 3 34 43 9 60 1 43 48 47 16 24 19 22 23 27 36 54 2 9 0 0 0 0 0 0 9 0 -------------------------------------------------------------------------------- /datasets/Nguyen_2016f/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 17 583 9911 220 2.22 209 0.358 114 0.196 1012 45 649 675 164 999 37 674 789 845 298 370 296 352 430 448 540 938 18 112 0 0 0 1 0 0 219 0 -------------------------------------------------------------------------------- /datasets/Oaks_2011/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Oaks JR. A time-calibrated species tree of Crocodylia reveals a recent radiation of the true crocodiles. Evolution. 2011 Nov 1;65(11):3285-97." 3 | year: 2011 4 | DOI: dx.doi.org/10.1111/j.1558-5646.2011.01373.x 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.5k9s0 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 79 12 | nchar: 7282 13 | datatype: nucleotide 14 | partitions: 50 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: "Crocodylia" 28 | english: "Crocodilians" 29 | taxon ID: 1294634 30 | notes: "The original dataset specified each exon for each of the nuclear coding genes. But many of these exons are very short, making it impractical to divide them up into codon positions, so I made the pragmatic decision to lump exons together." -------------------------------------------------------------------------------- /datasets/Oaks_2011/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 79 7282 575278 36778 6.393 2366 0.325 2184 0.3 0.523 0.477 140855 144607 112171 140746 10 2 34 58 10 7 0 0 0 0 0 0 0 13435 23343 -------------------------------------------------------------------------------- /datasets/Prebus_2017/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Prebus M (2017) Insights into the evolution, biogeography and natural history of the acorn ants, genus Temnothorax Mayr (hymenoptera: Formicidae). BMC Evolutionary Biology 17: 250. https://doi.org/10.1186/s12862-017-1095-8" 3 | year: 2017 4 | DOI: dx.doi.org/10.1186/s12862-017-1095-8 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.b464m 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 50 12 | nchar: 1561581 13 | datatype: nucleotide 14 | partitions: 2098 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: 35 mya 26 | study clade: 27 | latin: Temnothorax 28 | english: Acorn ants 29 | taxon ID: 300110 30 | notes: This is the tmno_50t_min90 dataset from Dryad. The UCE positions were inferred from the rcluster_50t_min90_part.txt file. 31 | -------------------------------------------------------------------------------- /datasets/Prebus_2017/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 50 1561581 78079050 5800673 7.429 702480 0.45 404463 0.259 0.562 0.438 20373358 15790272 15860371 20254376 0 0 0 0 0 0 0 0 0 0 0 0 0 2693639 3107034 -------------------------------------------------------------------------------- /datasets/Pyron_2011/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Pyron RA, Wiens JJ. A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Molecular Phylogenetics and Evolution. 2011 Nov 30;61(2):543-83." 3 | year: 2011 4 | DOI: dx.doi.org/10.1016/j.ympev.2011.06.012 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.vd0m7 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 2872 12 | nchar: 12712 13 | datatype: nucleotide 14 | partitions: 34 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 321.1 mya 25 | study root age: NA 26 | study clade: 27 | latin: "Amphibia" 28 | english: "amphibians" 29 | taxon ID: 8292 30 | notes: NA 31 | -------------------------------------------------------------------------------- /datasets/Pyron_2011/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 2872 12712 36508864 29152570 79.851 9018 0.709 7856 0.618 0.569 0.431 2281897 1745426 1450702 1873362 474 431 1204 2090 375 309 10 3 7 4 0 4736 0 29147834 0 -------------------------------------------------------------------------------- /datasets/Ran_2018_aa/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Ran J-H, Shen T-T, Wang M-M, Wang X-Q (2018) Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms. Proceedings of the Royal Society B 285(1881): 20181012." 3 | year: 2018 4 | DOI: dx.doi.org/10.1098/rspb.2018.1012 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.f7f57 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 38 12 | nchar: 432014 13 | datatype: protein 14 | partitions: 1308 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 313 mya 25 | study root age: 377 mya 26 | study clade: 27 | latin: Spermatophyta 28 | english: Seed Plants 29 | taxon ID: 58024 30 | notes: This is the amino acid dataset described in the paper. It was generated by translating the codon dataset in this repository Ran_2018_dna 31 | -------------------------------------------------------------------------------- /datasets/Ran_2018_aa/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex Abi 432014 3061 0.709 33617 6867 23351 29339 17995 29598 9319 24234 26933 43055 10185 15785 19595 15770 23338 29526 20620 30858 5790 13178 0 0 0 0 0 0 3061 0 3 | alignment.nex Aco 432014 3615 0.837 31986 6766 23880 29119 18268 29277 9070 24643 28056 42546 10156 16189 19405 15156 22355 30852 20558 31195 5628 13294 0 0 0 0 0 0 3615 0 4 | alignment.nex Ame 432014 3462 0.801 33512 6942 23348 29101 17985 29548 9498 24271 27145 42853 10335 16011 19407 15679 23114 29352 20443 30918 5805 13285 0 0 0 0 0 0 3462 0 5 | alignment.nex Ara 432014 3901 0.903 33887 6860 23183 29619 17788 29423 9380 23854 27267 42585 10420 15782 19604 15812 23191 28918 20337 31065 5804 13334 0 0 0 0 0 0 3901 0 6 | alignment.nex Ath 432014 2380 0.551 32338 6637 24069 29766 18267 29361 8823 24051 28674 42313 10300 16165 19403 14751 22436 31226 20937 31340 5576 13201 0 0 0 0 0 0 2380 0 7 | alignment.nex Atr 432014 12284 2.843 32122 6784 22983 28645 17858 29176 9218 23793 26524 42566 9989 15241 19432 14636 22838 29688 19477 30168 5596 12996 0 0 0 0 0 0 12284 0 8 | alignment.nex Bdi 432014 3340 0.773 35690 6727 24467 28513 17787 29988 9240 22797 26413 42554 10106 15029 20168 14795 23846 29844 20445 31673 5555 13037 0 0 0 0 0 0 3340 0 9 | alignment.nex Cep 432014 3310 0.766 33413 6938 23338 29212 18009 29520 9510 24302 27094 42984 10327 15982 19394 15688 23185 29421 20413 30837 5824 13313 0 0 0 0 0 0 3310 0 10 | alignment.nex Cga 432014 7574 1.753 33966 6842 23194 28570 17971 29124 9427 23376 26377 43200 10034 15105 19140 15521 23309 29650 20138 30790 5672 13034 0 0 0 0 0 0 7574 0 11 | alignment.nex Cun 432014 3843 0.89 33435 6838 23293 29343 17930 29495 9328 24276 27155 42912 10253 15997 19433 15764 23054 29334 20401 30860 5772 13298 0 0 0 0 0 0 3843 0 12 | alignment.nex Cyc 432014 3595 0.832 34218 6847 23153 29324 17882 29762 9456 24034 26446 43257 9952 15521 19604 15879 23873 28798 20244 31199 5865 13105 0 0 0 0 0 0 3595 0 13 | alignment.nex Eph 432014 5052 1.169 32326 6859 23369 29049 18227 28607 9200 24610 28186 42256 10171 16634 19187 15379 22466 30524 20601 30411 5630 13270 0 0 0 0 0 0 5052 0 14 | alignment.nex Fok 432014 4827 1.117 33129 6826 23289 29257 17917 29338 9342 24234 27193 42825 10270 16156 19325 15766 22770 29510 20310 30744 5740 13246 0 0 0 0 0 0 4827 0 15 | alignment.nex Gin 432014 3052 0.706 34114 6874 23242 29334 17854 29706 9388 23868 26786 43200 10177 15568 19606 15950 23648 28911 20471 31271 5840 13154 0 0 0 0 0 0 3052 0 16 | alignment.nex Gma 432014 2677 0.62 32959 6696 24100 28880 18415 29169 9206 24300 27709 42843 9758 16370 19767 15122 22638 30683 20169 31445 5668 13440 0 0 0 0 0 0 2677 0 17 | alignment.nex Gne 432014 6375 1.476 33323 7007 23416 28691 18100 28533 9378 24309 27471 42532 9925 16130 19083 15454 23025 29604 20098 30652 5637 13271 0 0 0 0 0 0 6375 0 18 | alignment.nex Lja 432014 30656 7.096 33560 6353 21819 26904 16639 27865 8862 20881 24796 41147 9214 13771 18558 15025 22061 27365 19372 29445 5512 12209 0 0 0 0 0 0 30656 0 19 | alignment.nex Ltu 432014 48196 11.156 29666 6144 21189 26150 16228 26645 8242 21717 24258 38450 9193 13869 17736 13518 20927 27307 18076 27728 5091 11684 0 0 0 0 0 0 48196 0 20 | alignment.nex Mac 432014 13797 3.194 32887 6770 23345 28100 17670 28698 9251 23728 25914 42323 9878 15027 19236 14426 23081 29522 19458 30398 5540 12965 0 0 0 0 0 0 13797 0 21 | alignment.nex Met 432014 2790 0.646 33390 6869 23291 29479 17993 29488 9410 24484 27391 42908 10275 16162 19408 15851 22935 29590 20400 30839 5777 13284 0 0 0 0 0 0 2790 0 22 | alignment.nex Nad 432014 27367 6.335 30935 6546 22300 27365 17346 27796 8936 22977 25205 40800 9602 14647 18431 14139 22249 29078 18806 29657 5376 12456 0 0 0 0 0 0 27367 0 23 | alignment.nex Nag 432014 2686 0.622 33297 7015 23437 29305 18008 29277 9509 24453 27479 42832 10349 16174 19415 15810 23005 29601 20378 30865 5799 13320 0 0 0 0 0 0 2686 0 24 | alignment.nex Osa 432014 7064 1.635 35658 6654 24136 28504 17627 29498 9134 22758 26255 41965 10031 15133 20071 14613 23779 29278 19977 31300 5548 13031 0 0 0 0 0 0 7064 0 25 | alignment.nex Paq 432014 27388 6.34 33488 6513 22245 27122 16972 28294 8889 20952 25040 41383 9485 14096 18275 15198 21982 27970 19289 30068 5400 11965 0 0 0 0 0 0 27388 0 26 | alignment.nex Pda 432014 56334 13.04 29657 6093 20766 25607 15827 25893 8166 21390 23590 37787 9080 13459 17352 13099 20624 26241 17294 27047 4997 11711 0 0 0 0 0 0 56334 0 27 | alignment.nex Pin 432014 4330 1.002 33467 6815 23202 29342 17902 29518 9263 24263 26925 42918 10038 15850 19526 15700 23325 29344 20514 30822 5753 13197 0 0 0 0 0 0 4330 0 28 | alignment.nex Pla 432014 3360 0.778 33213 6883 23298 29352 18006 29383 9391 24475 27387 42958 10260 16273 19401 15814 22907 29594 20315 30702 5761 13281 0 0 0 0 0 0 3360 0 29 | alignment.nex Pod 432014 3628 0.84 33236 6962 23491 29154 17931 29288 9490 24298 27372 42811 10334 16123 19441 15784 22994 29480 20353 30798 5755 13291 0 0 0 0 0 0 3628 0 30 | alignment.nex Pse 432014 5380 1.245 33311 6853 23277 28961 17889 29457 9470 24272 26956 42718 10231 15935 19341 15583 22985 29376 20302 30684 5770 13263 0 0 0 0 0 0 5380 0 31 | alignment.nex Ptr 432014 1876 0.434 32994 6789 24096 29190 18523 29633 9216 24369 28046 42780 10121 16100 19801 15150 22615 30589 20034 31257 5679 13156 0 0 0 0 0 0 1876 0 32 | alignment.nex Sci 432014 3517 0.814 33393 6954 23293 29336 17983 29363 9416 24293 27237 42886 10297 15920 19407 15714 23190 29327 20519 30900 5778 13291 0 0 0 0 0 0 3517 0 33 | alignment.nex Sly 432014 8006 1.853 32216 6751 23750 29016 17908 28946 8881 24054 27738 42069 10001 15971 19325 14719 22357 30325 20105 31013 5577 13286 0 0 0 0 0 0 8006 0 34 | alignment.nex Tax 432014 3017 0.698 33502 6916 23364 29228 17969 29564 9531 24329 27193 42943 10267 16025 19420 15661 23117 29460 20501 30868 5820 13319 0 0 0 0 0 0 3017 0 35 | alignment.nex Tor 432014 3996 0.925 33402 6864 23351 29071 18008 29529 9496 24257 27121 42813 10324 15994 19374 15653 23142 29354 20370 30825 5779 13291 0 0 0 0 0 0 3996 0 36 | alignment.nex Vvi 432014 18139 4.199 31913 6610 22842 28293 17637 28458 8976 23590 26307 41301 9822 15200 19125 14564 22238 29540 19207 30000 5514 12738 0 0 0 0 0 0 18139 0 37 | alignment.nex Wel 432014 3696 0.856 32883 7068 22990 29345 18207 28688 9558 24674 27696 43101 10009 16320 19362 15435 23291 30031 20309 30342 5684 13325 0 0 0 0 0 0 3696 0 38 | alignment.nex Zam 432014 5557 1.286 34388 6951 22948 29157 17754 29633 9485 23895 26234 43141 9876 15433 19525 15736 23807 28400 20015 31121 5840 13118 0 0 0 0 0 0 5557 0 39 | alignment.nex smi 432014 2008 0.465 33651 6839 23329 29497 18007 29719 9391 24333 27011 43211 10181 15824 19598 15778 23465 29601 20653 30896 5825 13197 0 0 0 0 0 0 2008 0 -------------------------------------------------------------------------------- /datasets/Ran_2018_aa/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 38 432014 16416532 355136 2.163 281961 0.653 228338 0.529 1258142 257522 881434 1093240 676287 1104258 350746 903394 1018580 1609726 381226 592971 732681 580092 869162 1116214 761909 1163001 214977 495834 0 0 0 0 0 0 355136 0 -------------------------------------------------------------------------------- /datasets/Ran_2018_dna/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Ran J-H, Shen T-T, Wang M-M, Wang X-Q (2018) Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms. Proceedings of the Royal Society B 285(1881): 20181012." 3 | year: 2018 4 | DOI: dx.doi.org/10.1098/rspb.2018.1012 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.f7f57 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 38 12 | nchar: 1296042 13 | datatype: nucleotide 14 | partitions: 3924 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 313 mya 25 | study root age: 377 mya 26 | study clade: 27 | latin: Spermatophyta 28 | english: Seed Plants 29 | taxon ID: 58024 30 | notes: This is the codon dataset described in the paper, that contains all three codon positions, in frame for each locus 31 | -------------------------------------------------------------------------------- /datasets/Ran_2018_dna/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex Abi 1296042 9183 0.709 0.562 0.438 368682 244679 318989 354509 0 0 0 0 0 0 0 0 0 0 0 0 0 9183 0 3 | alignment.nex Aco 1296042 10845 0.837 0.574 0.426 370849 237492 310231 366625 0 0 0 0 0 0 0 0 0 0 0 0 0 10845 0 4 | alignment.nex Ame 1296042 10386 0.801 0.565 0.435 369955 241417 317852 356432 0 0 0 0 0 0 0 0 0 0 0 0 0 10386 0 5 | alignment.nex Ara 1296042 11703 0.903 0.562 0.438 369456 242301 320131 352451 0 0 0 0 0 0 0 0 0 0 0 0 0 11703 0 6 | alignment.nex Ath 1296042 7140 0.551 0.555 0.445 362643 254401 318891 352967 0 0 0 0 0 0 0 0 0 0 0 0 0 7140 0 7 | alignment.nex Atr 1296042 36850 2.843 0.552 0.448 348445 247665 316808 346274 0 0 0 0 0 0 0 0 0 0 0 1 0 36849 0 8 | alignment.nex Bdi 1296042 10020 0.773 0.506 0.494 332766 295087 340690 317479 0 0 0 0 0 0 0 0 0 0 0 0 0 10020 0 9 | alignment.nex Cep 1296042 9930 0.766 0.565 0.435 370259 241287 317622 356944 0 0 0 0 0 0 0 0 0 0 0 0 0 9930 0 10 | alignment.nex Cga 1296042 22722 1.753 0.558 0.442 360428 244972 317684 350236 0 0 0 0 0 0 0 0 0 0 0 0 0 22722 0 11 | alignment.nex Cun 1296042 11529 0.89 0.568 0.432 371835 239070 316073 357535 0 0 0 0 0 0 0 0 0 0 0 0 0 11529 0 12 | alignment.nex Cyc 1296042 10785 0.832 0.558 0.442 363300 243953 324239 353765 0 0 0 0 0 0 0 0 0 0 0 0 0 10785 0 13 | alignment.nex Eph 1296042 15156 1.169 0.572 0.428 376921 240634 307130 356201 0 0 0 0 0 0 0 0 0 0 0 0 0 15156 0 14 | alignment.nex Fok 1296042 14481 1.117 0.57 0.43 372382 237834 313723 357622 0 0 0 0 0 0 0 0 0 0 0 0 0 14481 0 15 | alignment.nex Gin 1296042 9156 0.706 0.561 0.439 366672 243779 321403 355032 0 0 0 0 0 0 0 0 0 0 0 0 0 9156 0 16 | alignment.nex Gma 1296042 8031 0.62 0.556 0.444 358659 254040 317222 358090 0 0 0 0 0 0 0 0 0 0 0 0 0 8031 0 17 | alignment.nex Gne 1296042 19125 1.476 0.567 0.433 368852 241343 312001 354721 0 0 0 0 0 0 0 0 0 0 0 0 0 19125 0 18 | alignment.nex Lja 1296042 91968 7.096 0.543 0.457 332926 243575 306182 321391 0 0 0 0 0 0 0 0 0 0 0 0 0 91968 0 19 | alignment.nex Ltu 1296042 143498 11.072 0.534 0.466 313144 240004 297012 301993 26 39 119 133 26 46 0 0 2 0 0 2 0 143496 0 20 | alignment.nex Mac 1296042 41391 3.194 0.538 0.462 341185 261471 318036 333959 0 0 0 0 0 0 0 0 0 0 0 0 0 41391 0 21 | alignment.nex Met 1296042 8370 0.646 0.57 0.43 374368 238516 315444 359344 0 0 0 0 0 0 0 0 0 0 0 0 0 8370 0 22 | alignment.nex Nad 1296042 81246 6.269 0.545 0.455 333071 244248 308060 329115 28 22 106 86 27 32 0 0 1 0 0 6 0 81240 0 23 | alignment.nex Nag 1296042 8058 0.622 0.569 0.431 374128 238509 316003 359344 0 0 0 0 0 0 0 0 0 0 0 0 0 8058 0 24 | alignment.nex Osa 1296042 21192 1.635 0.508 0.492 331704 289905 336693 316548 0 0 0 0 0 0 0 0 0 0 0 0 0 21192 0 25 | alignment.nex Paq 1296042 82164 6.34 0.538 0.462 331554 247285 313637 321402 0 0 0 0 0 0 0 0 0 0 0 0 0 82164 0 26 | alignment.nex Pda 1296042 169000 13.04 0.54 0.46 307681 230776 287120 301465 0 0 0 0 0 0 0 0 0 0 0 1 0 168999 0 27 | alignment.nex Pin 1296042 12990 1.002 0.563 0.437 368474 242495 317731 354352 0 0 0 0 0 0 0 0 0 0 0 0 0 12990 0 28 | alignment.nex Pla 1296042 10080 0.778 0.57 0.43 374529 238659 314283 358491 0 0 0 0 0 0 0 0 0 0 0 0 0 10080 0 29 | alignment.nex Pod 1296042 10884 0.84 0.569 0.431 372791 238560 315388 358419 0 0 0 0 0 0 0 0 0 0 0 0 0 10884 0 30 | alignment.nex Pse 1296042 16140 1.245 0.564 0.436 368416 241435 316119 353932 0 0 0 0 0 0 0 0 0 0 0 0 0 16140 0 31 | alignment.nex Ptr 1296042 5628 0.434 0.562 0.438 362673 246346 319386 362009 0 0 0 0 0 0 0 0 0 0 0 0 0 5628 0 32 | alignment.nex Sci 1296042 10551 0.814 0.566 0.434 371471 240749 316761 356510 0 0 0 0 0 0 0 0 0 0 0 0 0 10551 0 33 | alignment.nex Sly 1296042 24018 1.853 0.566 0.434 362342 240563 311614 357505 0 0 0 0 0 0 0 0 0 0 0 0 0 24018 0 34 | alignment.nex Tax 1296042 9051 0.698 0.565 0.435 370922 242625 317449 355995 0 0 0 0 0 0 0 0 0 0 0 0 0 9051 0 35 | alignment.nex Tor 1296042 11988 0.925 0.565 0.435 369632 241369 317263 355790 0 0 0 0 0 0 0 0 0 0 0 0 0 11988 0 36 | alignment.nex Vvi 1296042 54417 4.199 0.553 0.447 345748 243543 310846 341488 0 0 0 0 0 0 0 0 0 0 0 6 0 54411 0 37 | alignment.nex Wel 1296042 11088 0.856 0.572 0.428 376212 240454 309551 358737 0 0 0 0 0 0 0 0 0 0 0 0 0 11088 0 38 | alignment.nex Zam 1296042 16671 1.286 0.556 0.444 360918 243756 324126 350571 0 0 0 0 0 0 0 0 0 0 0 0 0 16671 0 39 | alignment.nex smi 1296042 6024 0.465 0.562 0.438 369416 245038 320067 355497 0 0 0 0 0 0 0 0 0 0 0 0 0 6024 0 -------------------------------------------------------------------------------- /datasets/Ran_2018_dna/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 38 1296042 49249596 1063459 2.159 881125 0.68 777882 0.6 0.557 0.443 13645409 9329835 11999460 13210740 54 61 225 219 53 78 0 0 3 0 0 16 0 1063443 0 -------------------------------------------------------------------------------- /datasets/Reddy_2017/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Reddy S, Kimball RT, Pandey A, Hosner PA, Braun MJ, Hackett SJ, Han K, Harshman J, Huddleston CJ, Kingston S, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Witt CC, Yuri T, Braun EL (2017) Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling. Systematic Biology 66(5): 857-879." 3 | year: 2017 4 | DOI: dx.doi.org/10.1093/sysbio/syx041 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.6536v 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 235 12 | nchar: 137324 13 | datatype: nucleotide 14 | partitions: 88 15 | genomes: 16 | mitochondrial: no 17 | nuclear: no 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 111 mya 25 | study root age: NA 26 | study clade: 27 | latin: Aves 28 | english: Birds 29 | taxon ID: 8782 30 | notes: this is the dataset Reddy_sup_fileS5_EB2taxset.nex, which was used to produce figure 3 in the paper from this link https://datadryad.org/bitstream/handle/10255/dryad.141055/Reddy_sup_fileS5_alignments.tar.gz?sequence=1. The charsets in this repository are the main charsets derived from that file (88 in total). 31 | -------------------------------------------------------------------------------- /datasets/Reddy_2017/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 235 137324 32271140 24383025 75.557 56001 0.408 43010 0.313 0.553 0.447 2106342 1724660 1780618 2266227 799 715 3747 3471 890 635 5 1 5 0 0 194886 0 23988198 199941 -------------------------------------------------------------------------------- /datasets/Richart_2015/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Richart C, Hayashi C, Marshal H (2015) Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies. Molecular Phylogenetics and Evolution 95: 171–182" 3 | year: 2015 4 | DOI: dx.doi.org/10.1016/j.ympev.2015.11.010 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.3mr26 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 6 12 | nchar: 536124 13 | datatype: nucleotide 14 | partitions: 2016 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 258.8 mya 25 | study root age: NA 26 | study clade: 27 | latin: Ischyropsalidoidea 28 | english: harvestmen or daddy longlegs 29 | taxon ID: 101157 30 | notes: NA 31 | -------------------------------------------------------------------------------- /datasets/Richart_2015/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex Acuclavella 536124 2896 0.54 0.609 0.391 172104 96208 112393 152523 0 0 0 0 0 0 0 0 0 0 0 0 0 1911 985 3 | alignment.nex Hesperoneamstoma 536124 534795 99.752 0.497 0.503 370 325 344 290 0 0 0 0 0 0 0 0 0 0 0 534777 0 18 0 4 | alignment.nex Hesperonemastoma 536124 9792 1.826 0.57 0.43 161376 105060 121047 138849 0 0 0 0 0 0 0 0 0 0 0 0 0 3567 6225 5 | alignment.nex Ortholasma 536124 8848 1.65 0.562 0.438 159671 110685 120343 136577 0 0 0 0 0 0 0 0 0 0 0 0 0 2652 6196 6 | alignment.nex Sabacon 536124 2254 0.42 0.576 0.424 161421 106730 119778 145941 0 0 0 0 0 0 0 0 0 0 0 0 0 1812 442 7 | alignment.nex Trogulus 536124 12463 2.325 0.574 0.426 160071 104130 118932 140528 0 0 0 0 0 0 0 0 0 0 0 0 0 2778 9685 -------------------------------------------------------------------------------- /datasets/Richart_2015/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 6 536124 3216744 571048 17.752 231761 0.432 104700 0.195 0.565 0.435 815013 523138 592837 714708 0 0 0 0 0 0 0 0 0 0 0 534777 0 12738 23533 -------------------------------------------------------------------------------- /datasets/Rightmyer_2013/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Rightmyer MG, Griswold T, Brady SG. Phylogeny and systematics of the bee genus Osmia (Hymenoptera: Megachilidae) with emphasis on North American Melanosmia: subgenera, synonymies and nesting biology revisited. Systematic Entomology. 2013 Jul 1;38(3):561-76." 3 | year: 2013 4 | DOI: dx.doi.org/10.1111/syen.12013 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.jd5ff 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 94 12 | nchar: 3692 13 | datatype: nucleotide 14 | partitions: 25 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: "Hymenoptera: Megachilidae" 28 | english: "bee" 29 | taxon ID: 124286 30 | notes: NA -------------------------------------------------------------------------------- /datasets/Rightmyer_2013/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 94 3692 347048 55246 15.919 1431 0.388 1044 0.283 0.588 0.412 82478 59411 60379 89111 22 29 84 176 12 98 0 0 2 0 0 287 0 54959 0 -------------------------------------------------------------------------------- /datasets/Sauquet_2011/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Sauquet H, Ho SY, Gandolfo MA, Jordan GJ, Wilf P, Cantrill DJ, Bayly MJ, Bromham L, Brown GK, Carpenter RJ, Lee DM. Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales). Systematic Biology. 2012 Mar 1;61(2):289-313." 3 | year: 2012 4 | DOI: dx.doi.org/10.1093/sysbio/syr116 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.qq106tm4 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 51 12 | nchar: 5444 13 | datatype: nucleotide 14 | partitions: 10 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: yes 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 79 mya 25 | study root age: 72 mya 26 | study clade: 27 | latin: "Nothofagus" 28 | english: "southern beeches" 29 | taxon ID: 26779 30 | notes: NA 31 | -------------------------------------------------------------------------------- /datasets/Sauquet_2011/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex Alfaroa_williamsii 5444 3838 70.5 0.603 0.397 461 336 301 508 0 0 0 0 0 0 0 0 0 0 0 0 0 496 3342 3 | alignment.nex Alfaropsis_roxburghiana 5444 3821 70.187 0.608 0.392 465 335 301 522 0 0 0 0 0 0 0 0 0 0 0 0 0 479 3342 4 | alignment.nex Betula_platyphylla 5444 582 10.691 0.595 0.405 1455 938 1029 1438 0 0 0 2 0 0 0 0 0 0 0 0 0 582 0 5 | alignment.nex Carpinus_betulus 5444 605 11.113 0.593 0.407 1448 943 1027 1421 0 0 0 0 0 0 0 0 0 0 0 0 0 605 0 6 | alignment.nex Carya_illinoinensis 5444 2461 45.206 0.59 0.41 839 587 635 922 0 0 0 0 0 0 0 0 0 0 0 7 0 543 1911 7 | alignment.nex Castanea_sativa 5444 631 11.591 0.583 0.417 1410 955 1052 1396 0 0 0 0 0 0 0 0 0 0 0 0 0 631 0 8 | alignment.nex Casuarina_equisetifolia 5444 1503 27.608 0.575 0.425 1152 789 887 1113 0 0 0 0 0 0 0 0 0 0 0 0 0 510 993 9 | alignment.nex Chrysolepis_sempervirens 5444 2228 40.926 0.536 0.464 871 703 789 853 0 0 0 0 0 0 0 0 0 0 0 0 0 203 2025 10 | alignment.nex Comptonia_peregrina 5444 1404 25.79 0.576 0.424 1178 802 909 1151 0 0 0 0 0 0 0 0 0 0 0 0 0 411 993 11 | alignment.nex Cucumis_sativus 5444 1123 20.628 0.613 0.387 1328 774 900 1319 0 0 0 0 0 0 0 0 0 0 0 0 0 495 628 12 | alignment.nex Cyclocarya_paliurus 5444 669 12.289 0.599 0.401 1431 910 1007 1427 0 0 0 0 0 0 0 0 0 0 0 1 0 668 0 13 | alignment.nex Engelhardia_fenzelii 5444 1124 20.647 0.618 0.382 1335 764 885 1336 0 0 0 0 0 0 0 0 0 0 0 0 0 496 628 14 | alignment.nex Fagus_grandifolia 5444 1114 20.463 0.578 0.422 1265 863 965 1236 0 0 1 0 0 0 0 0 0 0 0 2 0 1112 0 15 | alignment.nex Juglans_nigra 5444 586 10.764 0.597 0.403 1456 924 1035 1443 0 0 0 0 0 0 0 0 0 0 0 0 0 586 0 16 | alignment.nex Lithocarpus_henryi 5444 889 16.33 0.58 0.42 1324 910 1002 1319 0 0 0 0 0 0 0 0 0 0 0 0 0 889 0 17 | alignment.nex Lotus_japonicus 5444 2156 39.603 0.595 0.405 1006 592 739 951 0 0 0 0 0 0 0 0 0 0 0 0 0 61 2095 18 | alignment.nex Morella_cerifera 5444 2260 41.514 0.579 0.421 937 649 692 905 0 0 1 0 0 0 0 0 0 0 0 1 0 1266 993 19 | alignment.nex Nothofagus_aequilateralis 5444 4019 73.824 0.596 0.404 418 296 280 431 0 0 0 0 0 0 0 0 0 0 0 0 0 1634 2385 20 | alignment.nex Nothofagus_alessandri 5444 526 9.662 0.589 0.411 1460 961 1062 1435 0 0 0 0 0 0 0 0 0 0 0 0 0 526 0 21 | alignment.nex Nothofagus_alpina 5444 2819 51.782 0.558 0.442 716 562 597 750 0 0 0 0 0 0 0 0 0 0 0 0 0 434 2385 22 | alignment.nex Nothofagus_antarctica 5444 580 10.654 0.59 0.41 1456 952 1041 1415 0 0 0 0 0 0 0 0 0 0 0 1 0 579 0 23 | alignment.nex Nothofagus_balansae 5444 2791 51.267 0.572 0.428 740 545 590 778 0 0 0 0 0 0 0 0 0 0 0 0 0 406 2385 24 | alignment.nex Nothofagus_baumanniae 5444 4539 83.376 0.671 0.329 313 156 142 294 0 0 0 0 0 0 0 0 0 0 0 0 0 1526 3013 25 | alignment.nex Nothofagus_betuloides 5444 2788 51.212 0.567 0.433 735 546 603 772 0 0 0 0 0 0 0 0 0 0 0 0 0 403 2385 26 | alignment.nex Nothofagus_brassii 5444 3578 65.724 0.527 0.473 470 413 469 514 0 0 0 0 0 0 0 0 0 0 0 0 0 200 3378 27 | alignment.nex Nothofagus_carrii 5444 4540 83.395 0.676 0.324 314 154 139 297 0 0 0 0 0 0 0 0 0 0 0 0 0 1527 3013 28 | alignment.nex Nothofagus_cliffortioides 5444 4539 83.376 0.674 0.326 309 156 139 301 0 0 0 0 0 0 0 0 0 0 0 0 0 1526 3013 29 | alignment.nex Nothofagus_codonandra 5444 3310 60.801 0.601 0.399 639 399 453 643 0 0 0 0 0 0 0 0 0 0 0 0 0 297 3013 30 | alignment.nex Nothofagus_cunninghamii 5444 615 11.297 0.583 0.417 1422 954 1059 1394 0 0 0 0 0 0 0 0 0 0 0 0 0 615 0 31 | alignment.nex Nothofagus_discoidea 5444 3311 60.819 0.6 0.4 638 400 454 641 0 0 0 0 0 0 0 0 0 0 0 0 0 298 3013 32 | alignment.nex Nothofagus_dombeyi 5444 2731 50.165 0.571 0.429 761 550 613 789 0 0 0 0 0 0 0 0 0 0 0 0 0 346 2385 33 | alignment.nex Nothofagus_fusca 5444 545 10.011 0.588 0.412 1459 963 1053 1424 0 0 0 0 0 0 0 0 0 0 0 0 0 545 0 34 | alignment.nex Nothofagus_glauca 5444 626 11.499 0.583 0.417 1421 952 1057 1388 0 0 0 0 0 0 0 0 0 0 0 0 0 626 0 35 | alignment.nex Nothofagus_grandis 5444 2790 51.249 0.576 0.424 751 540 585 778 0 0 0 0 0 0 0 0 0 0 0 0 0 405 2385 36 | alignment.nex Nothofagus_gunnii 5444 546 10.029 0.59 0.41 1462 954 1052 1430 0 0 0 0 0 0 0 0 0 0 0 0 0 546 0 37 | alignment.nex Nothofagus_menziesii 5444 614 11.278 0.584 0.416 1429 958 1052 1389 0 0 0 1 1 0 0 0 0 0 0 0 0 614 0 38 | alignment.nex Nothofagus_moorei 5444 615 11.297 0.584 0.416 1423 951 1059 1394 0 0 0 2 0 0 0 0 0 0 0 0 0 615 0 39 | alignment.nex Nothofagus_nitida 5444 546 10.029 0.589 0.411 1461 953 1062 1422 0 0 0 0 0 0 0 0 0 0 0 0 0 546 0 40 | alignment.nex Nothofagus_obliqua 5444 623 11.444 0.583 0.417 1418 955 1057 1391 0 0 0 0 0 0 0 0 0 0 0 0 0 623 0 41 | alignment.nex Nothofagus_perryi 5444 3578 65.724 0.528 0.472 470 412 469 515 0 0 0 0 0 0 0 0 0 0 0 0 0 200 3378 42 | alignment.nex Nothofagus_pumilio 5444 2783 51.12 0.567 0.433 738 546 605 772 0 0 0 0 0 0 0 0 0 0 0 0 0 398 2385 43 | alignment.nex Nothofagus_resinosa 5444 3578 65.724 0.524 0.476 460 412 477 517 0 0 0 0 0 0 0 0 0 0 0 0 0 200 3378 44 | alignment.nex Nothofagus_solandri 5444 546 10.029 0.589 0.411 1460 960 1053 1425 0 0 0 0 0 0 0 0 0 0 0 0 0 546 0 45 | alignment.nex Nothofagus_truncata 5444 545 10.011 0.589 0.411 1461 962 1052 1424 0 0 0 0 0 0 0 0 0 0 0 0 0 545 0 46 | alignment.nex Oreomunnea_mexicana 5444 3836 70.463 0.597 0.403 452 343 305 508 0 0 0 0 0 0 0 0 0 0 0 0 0 494 3342 47 | alignment.nex Phaseolous_vulgaris 5444 3569 65.558 0.603 0.397 582 329 416 548 0 0 0 0 0 0 0 0 0 0 0 0 0 121 3448 48 | alignment.nex Platycarya_strobilacea 5444 708 13.005 0.596 0.404 1419 911 1001 1404 0 0 0 0 1 0 0 0 0 0 0 2 0 706 0 49 | alignment.nex Quercus_rubra 5444 828 15.209 0.582 0.418 1349 922 1008 1337 0 0 0 0 0 0 0 0 0 0 0 0 0 828 0 50 | alignment.nex Rhoiptelea_chiliantha 5444 585 10.746 0.6 0.4 1465 921 1025 1448 0 0 0 0 0 0 0 0 0 0 0 1 0 584 0 51 | alignment.nex Ticodendron_incognitum 5444 1351 24.816 0.584 0.416 1210 788 914 1180 0 1 0 0 0 0 0 0 0 0 0 5 0 353 993 52 | alignment.nex Trigonobalanus_verticellata 5444 609 11.187 0.59 0.41 1421 945 1039 1430 0 0 0 0 0 0 0 0 0 0 0 1 0 608 0 -------------------------------------------------------------------------------- /datasets/Sauquet_2011/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 51 5444 277644 97101 34.973 1497 0.275 840 0.154 0.589 0.411 53063 35495 39137 52838 0 1 2 5 2 0 0 0 0 0 0 21 0 30453 66627 -------------------------------------------------------------------------------- /datasets/Seago_2011/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Seago AE, Giorgi JA, Li J, Ślipiński A. Phylogeny, classification and evolution of ladybird beetles (Coleoptera: Coccinellidae) based on simultaneous analysis of molecular and morphological data. Molecular Phylogenetics and Evolution. 2011 Jul 31;60(1):137-51." 3 | year: 2011 4 | DOI: dx.doi.org/10.1016/j.ympev.2011.03.015 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.dc1r2 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 97 12 | nchar: 2253 13 | datatype: nucleotide 14 | partitions: 7 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: "Coccinellidae" 28 | english: "ladybirds" 29 | taxon ID: 7080 30 | notes: "alignment was edited to remove morphological data and taxa with no nucleotide data. Reduced taxa from 116 to 97" -------------------------------------------------------------------------------- /datasets/Seago_2011/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 97 2253 218541 52235 23.902 1313 0.583 1115 0.495 0.607 0.393 47921 31472 32718 54180 0 1 4 7 2 1 0 0 0 0 0 14 0 52221 0 -------------------------------------------------------------------------------- /datasets/Sharanowski_2011/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Sharanowski BJ, Dowling AP, Sharkey MJ. Molecular phylogenetics of Braconidae (Hymenoptera: Ichneumonoidea), based on multiple nuclear genes, and implications for classification. Systematic Entomology. 2011 Jul 1;36(3):549-72." 3 | year: 2011 4 | DOI: dx.doi.org/10.1111/j.1365-3113.2011.00580.x 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.1688p 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 139 12 | nchar: 3982 13 | datatype: nucleotide 14 | partitions: 11 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: "Braconidae" 28 | english: "parasitoid wasps" 29 | taxon ID: 7402 30 | notes: NA 31 | -------------------------------------------------------------------------------- /datasets/Sharanowski_2011/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 139 3982 553498 102685 18.552 2166 0.544 1674 0.42 0.539 0.461 125929 91376 115464 117518 64 54 117 141 69 79 1 0 1 0 0 162 0 28407 74116 -------------------------------------------------------------------------------- /datasets/Shen_2018/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Shen, X. X., Opulente, D. A., Kominek, J., Zhou, X., Steenwyk, J. L., Buh, K. V., ... & Boudouris, J. T. (2018). Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum. Cell, 175(6), 1533-1545." 3 | year: 2018 4 | DOI: dx.doi.org/10.1016/j.cell.2018.10.023 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.6084/m9.figshare.5854692 8 | license: "CCBY" 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 343 12 | nchar: 1162805 13 | datatype: protein 14 | partitions: 2407 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: 404 mya 26 | study clade: 27 | latin: "Saccharomycotina" 28 | english: "budding yeasts" 29 | taxon ID: 147537 30 | notes: "This alignment is that used to infer the tree in Figure 1, which is named '343_2408OGs.fasta' in the FigShare repository" 31 | -------------------------------------------------------------------------------- /datasets/Shen_2018/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 343 1162805 398842115 59645433 14.955 1084538 0.933 1049263 0.902 20943650 4250142 20112852 22843125 15619555 17885197 7077371 22945011 24126275 35369018 6794353 16915831 13549030 12876032 15888277 26636225 18021995 21687143 3905470 11750130 0 0 0 41729773 0 0 17915660 0 -------------------------------------------------------------------------------- /datasets/Siler_2013/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Siler CD, Oliveros CH, Santanen A, Brown RM. Multilocus phylogeny reveals unexpected diversification patterns in Asian wolf snakes (genus Lycodon). Zoologica Scripta. 2013 May 1;42(3):262-77." 3 | year: 2013 4 | DOI: dx.doi.org/10.1111/zsc.12007 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.cp6gg 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 61 12 | nchar: 2697 13 | datatype: nucleotide 14 | partitions: 7 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 40.2 mya 25 | study root age: NA 26 | study clade: 27 | latin: "Lycodon" 28 | english: "wolf snakes" 29 | taxon ID: 39095 30 | notes: NA -------------------------------------------------------------------------------- /datasets/Siler_2013/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 61 2697 164517 53816 32.712 792 0.294 665 0.247 0.593 0.407 34488 27248 17994 30931 2 7 10 14 1 6 0 0 0 0 0 0 0 18620 35196 -------------------------------------------------------------------------------- /datasets/Smith_2014/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Smith BT, Harvey MG, Faircloth BC, Glenn TC, Brumfield RT (2013) Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales. Systematic Biology 63(1): 83-95." 3 | year: 2013 4 | DOI: dx.doi.org/10.1093/sysbio/syt061 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.qm4j1.3 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 8 12 | nchar: 825804 13 | datatype: nucleotide 14 | partitions: 1366 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: 2.75 mya 26 | study clade: 27 | latin: Xenops minutus 28 | english: Plain xenops 29 | taxon ID: 255386 30 | notes: This is one of the five within-species datasets collected for the above study, and comprises the UCEs from that study. In the original study the data were analysed with species-tree methods, and not concatenated. 31 | -------------------------------------------------------------------------------- /datasets/Smith_2014/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex Xenopsminutus025_CH 825804 51881 6.282 0.6 0.4 232563 154255 154908 231621 47 58 198 172 59 42 0 0 0 0 0 32222 0 16494 3165 3 | alignment.nex Xenopsminutus102_SA 825804 57956 7.018 0.601 0.399 230912 152406 153287 230357 65 71 307 298 92 53 0 0 0 0 0 39165 0 17411 1380 4 | alignment.nex Xenopsminutus103_NA 825804 156145 18.908 0.601 0.399 201194 133144 133999 200675 61 55 198 208 56 69 0 0 0 0 0 104282 0 38000 13863 5 | alignment.nex Xenopsminutus104_CA 825804 128307 15.537 0.6 0.4 209027 139201 139978 208943 39 39 102 105 30 33 0 0 0 0 0 83993 0 34317 9997 6 | alignment.nex Xenopsminutus110_CH 825804 37989 4.6 0.601 0.399 236972 156619 157210 236256 57 77 279 217 78 50 0 0 0 0 0 24650 0 11651 1688 7 | alignment.nex Xenopsminutus111_SA 825804 145644 17.637 0.6 0.4 204100 135536 136080 203873 60 53 167 201 52 38 0 0 0 0 0 94013 0 40222 11409 8 | alignment.nex Xenopsminutus118_NA 825804 181216 21.944 0.598 0.402 192600 129221 129710 192578 58 50 152 137 48 34 0 0 0 0 0 117986 0 52413 10817 9 | alignment.nex Xenopsminutus119_CA 825804 120253 14.562 0.601 0.399 212571 140234 140943 211504 39 27 81 99 31 22 0 0 0 0 0 76020 0 33175 11058 -------------------------------------------------------------------------------- /datasets/Smith_2014/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 8 825804 6606432 879391 13.311 4489 0.005 1669 0.002 0.6 0.4 1719939 1140616 1146115 1715807 426 430 1484 1437 446 341 0 0 0 0 0 572331 0 243683 63377 -------------------------------------------------------------------------------- /datasets/Tolley_2013/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Tolley KA, Townsend TM, Vences M. Large-scale phylogeny of chameleons suggests African origins and Eocene diversification. Proceedings of the Royal Society of London B: Biological Sciences. 2013 May 22;280(1759):20130184." 3 | year: 2013 4 | DOI: dx.doi.org/10.1098/rspb.2013.0184 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.11350 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 203 12 | nchar: 5054 13 | datatype: nucleotide 14 | partitions: 16 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 56.7 mya 25 | study root age: 65 mya 26 | study clade: 27 | latin: "Chamaeleonidae" 28 | english: "chameleons" 29 | taxon ID: 40248 30 | notes: NA 31 | -------------------------------------------------------------------------------- /datasets/Tolley_2013/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 203 5054 1025962 237339 23.133 3846 0.761 3358 0.664 0.577 0.423 261354 192237 142601 192022 32 36 151 134 34 21 0 1 0 0 0 0 0 191486 45853 -------------------------------------------------------------------------------- /datasets/Unmack_2013/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Unmack PJ, Allen GR, Johnson JB. Phylogeny and biogeography of rainbowfishes (Melanotaeniidae) from Australia and New Guinea. Molecular Phylogenetics and Evolution. 2013 Apr 30;67(1):15-27." 3 | year: 2013 4 | DOI: dx.doi.org/10.1016/j.ympev.2012.12.019 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.qq846 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 139 12 | nchar: 6827 13 | datatype: nucleotide 14 | partitions: 25 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: 75 mya 26 | study clade: 27 | latin: "Melanotaeniidae" 28 | english: "rainbowfish" 29 | taxon ID: 30700 30 | notes: NA 31 | -------------------------------------------------------------------------------- /datasets/Unmack_2013/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 139 6827 948953 115678 12.19 3607 0.528 3185 0.467 0.54 0.46 212017 258268 126666 236278 3 6 13 13 6 5 0 0 0 0 0 0 0 18102 97576 -------------------------------------------------------------------------------- /datasets/Varga_2019/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Varga, T., Krizsán, K., Földi, C., Dima, B., Sánchez-García, M., Sánchez-Ramírez, S., et al. (2019). Megaphylogeny resolves global patterns of mushroom evolution. Nature Ecology and Evolution." 3 | year: 2019 4 | DOI: dx.doi.org/10.1038/s41559-019-0834-1 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.gc2k9r9 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 5285 12 | nchar: 5737 13 | datatype: nucleotide 14 | partitions: 3 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: Basidiomycota 28 | english: Mushrooms 29 | taxon ID: 5204 30 | notes: This is the dataset with excluded sites removed. The alignment file is "5284taxa_ML_alignment_exclude.txt" from this download https://datadryad.org/bitstream/handle/10255/dryad.203726/Varga_2019_NEE_5284taxa_MaximumLikelihood_analysis.zip?sequence=1. Illegal nexus characters in the alignment (e.g. '/') were replaced with underscores. It was not possible to identify all outgroup species from the published manuscript. 31 | -------------------------------------------------------------------------------- /datasets/Varga_2019/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 5284 5737 30314308 23594271 77.832 4236 0.738 3186 0.555 0.506 0.494 1791635 1433528 1900467 1590562 240 222 1035 1864 239 210 7 8 10 10 0 0 0 23594271 0 -------------------------------------------------------------------------------- /datasets/Wainwright_2012/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Wainwright PC, Smith WL, Price SA, Tang KL, Sparks JS, Ferry LA, Kuhn KL, Eytan RI, Near TJ. The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond. Systematic Biology. 2012 Dec 1;61(6):1001-27." 3 | year: 2012 4 | DOI: dx.doi.org/10.1093/sysbio/sys060 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.5h951h04 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 188 12 | nchar: 8439 13 | datatype: nucleotide 14 | partitions: 30 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 144.4 mya 25 | study root age: NA 26 | study clade: 27 | latin: "Acanthomorpha" 28 | english: "Acanthomorph fishes" 29 | taxon ID: 123368 30 | notes: NA 31 | -------------------------------------------------------------------------------- /datasets/Wainwright_2012/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 188 8439 1586532 171228 10.793 4468 0.529 3805 0.451 0.454 0.546 341960 391974 380633 299964 48 54 215 376 37 42 0 0 0 1 0 92 0 17684 153452 -------------------------------------------------------------------------------- /datasets/Whelan_2017/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Whelan, N.V., Kocot, K.M., Moroz, T.P., Mukherjee, K., Williams, P., Paulay, G., Moroz, L.L. and Halanych, K.M., 2017. Ctenophore relationships and their placement as the sister group to all other animals. Nature ecology & evolution, 1(11), p.1737." 3 | year: 2017 4 | DOI: dx.doi.org/10.1038/s41559-017-0381-6 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.6084/m9.figshare.4484138.v1 8 | license: CCBY 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 76 12 | nchar: 49388 13 | datatype: protein 14 | partitions: 127 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: NA 26 | study clade: 27 | latin: Metazoa 28 | english: Animals 29 | taxon ID: 33208 30 | notes: No study root age is given, becuase the root of the ingroup was used as a calibration. Thanks to Nathan V Whelan for confirming the gene boundaries in the dataset. 31 | -------------------------------------------------------------------------------- /datasets/Whelan_2017/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 76 49388 3753488 1982113 52.807 42240 0.855 35590 0.721 124057 33189 95355 119682 76319 94584 46940 107352 122403 188317 46630 68441 66468 72645 100969 110364 90072 126552 19459 61577 0 0 0 0 0 0 1982113 0 -------------------------------------------------------------------------------- /datasets/Wood_2012/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Wood HM, Matzke NJ, Gillespie RG, Griswold CE. Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders. Systematic Biology. 2012 Nov 28:sys092." 3 | year: 2012 4 | DOI: dx.doi.org/10.1093/sysbio/sys092 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.7231d 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 37 12 | nchar: 5185 13 | datatype: nucleotide 14 | partitions: 8 15 | genomes: 16 | mitochondrial: yes 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: 276.5 mya 26 | study clade: 27 | latin: "Archaeidae" 28 | english: "pelican spiders" 29 | taxon ID: 336678 30 | notes: "I removed the morphological data and adjusted the partition definitions accordingly. The original file contained two partitions for 28S, but nothing in the dryad package or the manuscript explained what these were. As a result, I joined these two partitions together here." -------------------------------------------------------------------------------- /datasets/Wood_2012/alignment.nex-seq-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex Afrarchaea_grimaldii 5185 5185 100.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5185 0 3 | alignment.nex Afrarchaea_pilgrimsrest_hw59Af3 5185 1650 31.823 0.473 0.527 781 849 1014 891 0 0 0 0 0 0 0 0 0 0 0 0 0 1650 0 4 | alignment.nex Afrarchaea_woodae_hw57Af1 5185 1368 26.384 0.477 0.523 848 890 1105 972 0 0 1 1 0 0 0 0 0 0 0 0 0 1368 0 5 | alignment.nex Aotearoa_magna_hw0050 5185 1061 20.463 0.499 0.501 969 921 1144 1090 0 0 0 0 0 0 0 0 0 0 0 0 0 1061 0 6 | alignment.nex Araneus_sp 5185 2114 40.771 0.524 0.476 766 663 796 842 0 0 0 1 2 1 0 0 0 0 0 0 0 2113 1 7 | alignment.nex Archaea_paradoxa 5185 5185 100.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5185 0 8 | alignment.nex Austrarchaea_davisae_hwAu066 5185 836 16.123 0.438 0.562 896 1100 1345 1006 0 0 0 2 0 0 0 0 0 0 0 0 0 836 0 9 | alignment.nex Austrarchaea_mainae_hw0075 5185 2257 43.529 0.484 0.516 656 664 847 760 0 0 0 1 0 0 0 0 0 0 0 0 0 2257 0 10 | alignment.nex Austrarchaea_nodosa_hw0074 5185 1818 35.063 0.483 0.517 776 753 987 851 0 0 0 0 0 0 0 0 0 0 0 0 0 1818 0 11 | alignment.nex Badumna_longinqua 5185 2056 39.653 0.471 0.529 692 767 889 781 0 0 0 0 0 0 0 0 0 0 0 0 0 2054 2 12 | alignment.nex Baltarchaea_conica 5185 5185 100.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5185 0 13 | alignment.nex Chilarchaea_quellon_hw0029 5185 1177 22.7 0.505 0.495 926 891 1093 1098 0 0 0 0 0 0 0 0 0 0 0 0 0 1177 0 14 | alignment.nex Dysdera_sp 5185 1734 33.443 0.489 0.511 777 779 983 912 0 0 0 0 0 0 0 0 0 0 0 0 0 1734 0 15 | alignment.nex Eriauchenius_bourgini_hw0061 5185 3839 74.041 0.546 0.454 324 283 326 411 0 0 1 0 1 0 0 0 0 0 0 0 0 3839 0 16 | alignment.nex Eriauchenius_workmani_hw0006 5185 1443 27.83 0.449 0.551 806 944 1114 874 0 0 0 2 1 1 0 0 0 0 0 0 0 1441 2 17 | alignment.nex Gnaphosidae_sp 5185 2069 39.904 0.478 0.522 721 767 858 770 0 0 0 0 0 0 0 0 0 0 0 0 0 2063 6 18 | alignment.nex Hickmania_troglodytes 5185 1685 32.498 0.503 0.497 794 775 949 950 3 3 9 13 3 1 0 0 0 0 0 0 0 1685 0 19 | alignment.nex Holarchaea_sp 5185 1993 38.438 0.543 0.457 832 672 788 900 0 0 0 0 0 0 0 0 0 0 0 0 0 1993 0 20 | alignment.nex Huttonia_sp_hwHutt41 5185 1908 36.798 0.511 0.489 790 720 878 878 0 2 2 3 0 3 1 0 0 0 0 0 0 1908 0 21 | alignment.nex Hypochilus_pococki 5185 2918 56.278 0.482 0.518 493 515 659 600 0 0 0 0 0 0 0 0 0 0 0 0 0 2918 0 22 | alignment.nex Kukulcania_hibernalis_hw 5185 2008 38.727 0.491 0.509 760 715 900 801 0 0 0 0 1 0 0 0 0 0 0 0 0 2008 0 23 | alignment.nex Loxosceles_sp 5185 1522 29.354 0.479 0.521 837 866 1044 916 0 0 0 0 0 0 0 0 0 0 0 0 0 1522 0 24 | alignment.nex Lycosidae_sp 5185 2051 39.556 0.488 0.512 733 752 852 797 0 0 0 0 0 0 0 0 0 0 0 0 0 2051 0 25 | alignment.nex Mecysmauchenius_segmentatus_hw 5185 1137 21.929 0.515 0.485 961 884 1078 1125 0 0 0 0 0 0 0 0 0 0 0 0 0 1137 0 26 | alignment.nex Mesarchaea_bell_hw0040_20A 5185 1510 29.122 0.51 0.49 870 791 1009 1005 0 0 0 0 0 0 0 0 0 0 0 0 0 1510 0 27 | alignment.nex Mimetus_sp 5185 2271 43.799 0.491 0.509 658 663 819 772 1 0 0 1 0 0 0 0 0 0 0 0 0 2271 0 28 | alignment.nex Myrmecarchaea_sp 5185 5185 100.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5185 0 29 | alignment.nex NewGenus_jeanneli_hw0057 5185 1652 31.861 0.479 0.521 800 827 1011 893 0 0 1 0 1 0 0 0 0 0 0 0 0 1652 0 30 | alignment.nex NewGenus_lavatenda_hw0003AB 5185 1690 32.594 0.459 0.541 738 849 1041 867 0 0 0 0 0 0 0 0 0 0 0 0 0 1690 0 31 | alignment.nex NewGenus_legendrei_hw0014 5185 1704 32.864 0.464 0.536 763 838 1025 852 0 0 1 1 1 0 0 0 0 0 0 0 0 1701 3 32 | alignment.nex Palpimanus_sp_hw0082 5185 1075 20.733 0.529 0.471 1014 823 1059 1097 8 11 32 47 7 12 0 0 0 0 0 0 0 1075 0 33 | alignment.nex Pararchaeidae_sp 5185 2992 57.705 0.508 0.492 526 491 587 588 0 1 0 0 0 0 0 0 0 0 0 0 0 2992 0 34 | alignment.nex Patarchaea_muralis 5185 5185 100.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5185 0 35 | alignment.nex Stegodyphus_sp_hwSteg42 5185 1925 37.126 0.538 0.462 852 682 825 901 0 0 0 0 0 0 0 0 0 0 0 0 0 1925 0 36 | alignment.nex Stenochilus_sp_hw0081 5185 1920 37.03 0.455 0.545 715 829 947 770 1 0 2 1 0 0 0 0 0 0 0 0 0 1920 0 37 | alignment.nex Uroctea_sp 5185 1639 31.61 0.5 0.5 837 788 985 936 0 0 0 0 0 0 0 0 0 0 0 0 0 1639 0 38 | alignment.nex Zearchaea_sp_hw0051 5185 1523 29.373 0.514 0.486 892 792 985 991 0 1 1 0 0 0 0 0 0 0 0 0 0 1523 0 -------------------------------------------------------------------------------- /datasets/Wood_2012/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 37 5185 191845 84470 44.03 2690 0.519 1792 0.346 0.426 0.574 24803 24543 29942 27897 13 18 50 73 17 18 1 0 0 0 0 0 0 84456 14 -------------------------------------------------------------------------------- /datasets/Worobey_2014a/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257." 3 | year: 2014 4 | DOI: dx.doi.org/10.1038/nature13016 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.m04j9 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 146 12 | nchar: 1716 13 | datatype: nucleotide 14 | partitions: 3 15 | genomes: 16 | mitochondrial: no 17 | nuclear: no 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: yes 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: 0.000156 mya 26 | study clade: 27 | latin: Influenzavirus A 28 | english: Influenza A virus 29 | taxon ID: 197911 30 | notes: This is the H7 gene from figure 2 in the ms. Root age is the oldest node in the tree, taken from the MCC trees on Dryad. Note that the dates of the names represent sampling dates that can be used for tip dating analyses. See original paper and repository for details. 31 | -------------------------------------------------------------------------------- /datasets/Worobey_2014a/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 146 1716 250536 4688 1.871 959 0.559 824 0.48 0.573 0.427 82732 45519 59454 58139 0 0 3 1 0 0 0 0 0 0 0 0 0 4688 0 -------------------------------------------------------------------------------- /datasets/Worobey_2014b/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257." 3 | year: 2014 4 | DOI: dx.doi.org/10.1038/nature13016 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.m04j9 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 327 12 | nchar: 759 13 | datatype: nucleotide 14 | partitions: 3 15 | genomes: 16 | mitochondrial: no 17 | nuclear: no 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: yes 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: 0.000163 mya 26 | study clade: 27 | latin: Influenzavirus A 28 | english: Influenza A virus 29 | taxon ID: 197911 30 | notes: This is the MP gene from figure 2 in the ms. Root age is the oldest node in the tree, taken from the MCC trees on Dryad. Note that the dates of the names represent sampling dates that can be used for tip dating analyses. See original paper and repository for details. 31 | -------------------------------------------------------------------------------- /datasets/Worobey_2014b/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 327 759 248193 1 0.0 389 0.513 361 0.476 0.504 0.496 72676 56724 66285 52490 0 0 12 5 0 0 0 0 0 0 0 1 0 0 0 -------------------------------------------------------------------------------- /datasets/Worobey_2014c/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257." 3 | year: 2014 4 | DOI: dx.doi.org/10.1038/nature13016 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.m04j9 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 92 12 | nchar: 1416 13 | datatype: nucleotide 14 | partitions: 3 15 | genomes: 16 | mitochondrial: no 17 | nuclear: no 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: yes 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: 0.000175 mya 26 | study clade: 27 | latin: Influenzavirus A 28 | english: Influenza A virus 29 | taxon ID: 197911 30 | notes: This is the N7 gene from figure 2 in the ms. Root age is the oldest node in the tree, taken from the MCC trees on Dryad. Note that the dates of the names represent sampling dates that can be used for tip dating analyses. See original paper and repository for details. 31 | -------------------------------------------------------------------------------- /datasets/Worobey_2014c/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 92 1416 130272 613 0.471 684 0.483 618 0.436 0.572 0.428 44039 25141 30365 30109 0 0 3 2 0 0 0 0 0 0 0 0 0 613 0 -------------------------------------------------------------------------------- /datasets/Worobey_2014d/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257." 3 | year: 2014 4 | DOI: dx.doi.org/10.1038/nature13016 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.m04j9 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 355 12 | nchar: 1497 13 | datatype: nucleotide 14 | partitions: 3 15 | genomes: 16 | mitochondrial: no 17 | nuclear: no 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: yes 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: 0.000245 mya 26 | study clade: 27 | latin: Influenzavirus A 28 | english: Influenza A virus 29 | taxon ID: 197911 30 | notes: This is the NP gene from figure 2 in the ms. Root age is the oldest node in the tree, taken from the MCC trees on Dryad. Note that the dates of the names represent sampling dates that can be used for tip dating analyses. See original paper and repository for details. 31 | -------------------------------------------------------------------------------- /datasets/Worobey_2014d/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 355 1497 531435 112 0.021 863 0.576 784 0.524 0.531 0.469 169911 105699 143216 112482 2 1 7 2 0 3 0 0 0 0 0 0 0 112 0 -------------------------------------------------------------------------------- /datasets/Worobey_2014e/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257." 3 | year: 2014 4 | DOI: dx.doi.org/10.1038/nature13016 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.m04j9 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 340 12 | nchar: 699 13 | datatype: nucleotide 14 | partitions: 3 15 | genomes: 16 | mitochondrial: no 17 | nuclear: no 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: yes 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: 0.000281 mya 26 | study clade: 27 | latin: Influenzavirus A 28 | english: Influenza A virus 29 | taxon ID: 197911 30 | notes: This is the NS gene from figure 2 in the ms. Root age is the oldest node in the tree, taken from the MCC trees on Dryad. Note that the dates of the names represent sampling dates that can be used for tip dating analyses. See original paper and repository for details. 31 | -------------------------------------------------------------------------------- /datasets/Worobey_2014e/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 340 699 237660 3209 1.35 504 0.721 461 0.66 0.542 0.458 72097 49570 57771 55011 0 1 0 1 0 0 0 0 0 0 0 1 0 3208 0 -------------------------------------------------------------------------------- /datasets/Worobey_2014f/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257." 3 | year: 2014 4 | DOI: dx.doi.org/10.1038/nature13016 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.m04j9 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 332 12 | nchar: 2151 13 | datatype: nucleotide 14 | partitions: 3 15 | genomes: 16 | mitochondrial: no 17 | nuclear: no 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: yes 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: 0.000403 mya 26 | study clade: 27 | latin: Influenzavirus A 28 | english: Influenza A virus 29 | taxon ID: 197911 30 | notes: This is the PA1/2 gene from figure 2 in the ms. Root age is the oldest node in the tree, taken from the MCC trees on Dryad. Note that the dates of the names represent sampling dates that can be used for tip dating analyses. See original paper and repository for details. 31 | -------------------------------------------------------------------------------- /datasets/Worobey_2014f/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 332 2151 714132 54 0.008 1248 0.58 1124 0.523 0.567 0.433 237665 137876 171501 167024 0 0 7 5 0 0 0 0 0 0 0 2 0 52 0 -------------------------------------------------------------------------------- /datasets/Worobey_2014g/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257." 3 | year: 2014 4 | DOI: dx.doi.org/10.1038/nature13016 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.m04j9 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 326 12 | nchar: 2274 13 | datatype: nucleotide 14 | partitions: 3 15 | genomes: 16 | mitochondrial: no 17 | nuclear: no 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: yes 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: 0.000289 mya 26 | study clade: 27 | latin: Influenzavirus A 28 | english: Influenza A virus 29 | taxon ID: 197911 30 | notes: This is the PB1 gene from figure 2 in the ms. Root age is the oldest node in the tree, taken from the MCC trees on Dryad. Note that the dates of the names represent sampling dates that can be used for tip dating analyses. See original paper and repository for details. 31 | -------------------------------------------------------------------------------- /datasets/Worobey_2014g/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 326 2274 741324 13 0.002 1210 0.532 1096 0.482 0.573 0.427 258577 146407 169898 166385 1 3 14 24 0 2 0 0 0 0 0 3 0 10 0 -------------------------------------------------------------------------------- /datasets/Worobey_2014h/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: "Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257." 3 | year: 2014 4 | DOI: dx.doi.org/10.1038/nature13016 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.5061/dryad.m04j9 8 | license: CC0 9 | used for tree inference: yes 10 | alignment: 11 | ntax: 351 12 | nchar: 2280 13 | datatype: nucleotide 14 | partitions: 3 15 | genomes: 16 | mitochondrial: no 17 | nuclear: no 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: yes 23 | bacterial: no 24 | timetree root age: NA 25 | study root age: 0.000393 mya 26 | study clade: 27 | latin: Influenzavirus A 28 | english: Influenza A virus 29 | taxon ID: 197911 30 | notes: This is the PB2 gene from figure 2 in the ms. Root age is the oldest node in the tree, taken from the MCC trees on Dryad. Note that the dates of the names represent sampling dates that can be used for tip dating analyses. See original paper and repository for details. 31 | -------------------------------------------------------------------------------- /datasets/Worobey_2014h/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 351 2280 800280 27 0.003 1390 0.61 1250 0.548 0.56 0.44 272020 149458 202916 175805 1 6 21 24 0 2 0 0 0 0 0 0 0 27 0 -------------------------------------------------------------------------------- /datasets/Wu_2018_aa/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: 'Wu, S., Edwards, S., & Liu, L. (2018). Genome-scale DNA sequence data and the evolutionary history of placental mammals. Data in brief, 18, 1972-1975.' 3 | year: 2018 4 | DOI: dx.doi.org/10.1016/j.dib.2018.04.094 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.6084/m9.figshare.6031190.v2 8 | license: CCBY 9 | used for tree inference: no 10 | alignment: 11 | ntax: 90 12 | nchar: 3050199 13 | datatype: protein 14 | partitions: 5162 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 177 mya 25 | study root age: NA 26 | study clade: 27 | latin: mammalia 28 | english: mammals 29 | taxon ID: 40674 30 | notes: This is the cds_5162.zip dataset. The amino acid dataset was produced by translating each locus. 31 | -------------------------------------------------------------------------------- /datasets/Wu_2018_aa/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ? 2 | alignment.nex 90 3050199 274517910 42704015 15.556 2203490 0.722 1474177 0.483 15113234 4896631 11880989 16991700 8702272 13647656 6055384 10902500 14644717 23107239 5085747 9179181 13058629 11160747 12460889 19231042 12199513 14267321 2681664 6546840 0 0 0 0 0 0 25246277 17457738 -------------------------------------------------------------------------------- /datasets/Wu_2018_dna/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: 'Wu, S., Edwards, S., & Liu, L. (2018). Genome-scale DNA sequence data and the evolutionary history of placental mammals. Data in brief, 18, 1972-1975.' 3 | year: 2018 4 | DOI: dx.doi.org/10.1016/j.dib.2018.04.094 5 | 6 | dataset: 7 | DOI: dx.doi.org/10.6084/m9.figshare.6031190.v2 8 | license: CCBY 9 | used for tree inference: no 10 | alignment: 11 | ntax: 90 12 | nchar: 9150597 13 | datatype: nucleotide 14 | partitions: 15486 15 | genomes: 16 | mitochondrial: no 17 | nuclear: yes 18 | chloroplast: no 19 | dsDNA: no 20 | ssDNA: no 21 | dsRNA: no 22 | ssRNA: no 23 | bacterial: no 24 | timetree root age: 177 mya 25 | study root age: NA 26 | study clade: 27 | latin: mammalia 28 | english: mammals 29 | taxon ID: 40674 30 | notes: This is the cds_5162.zip dataset, loci were in frame and codon positions were annotated as such. 31 | -------------------------------------------------------------------------------- /datasets/Wu_2018_dna/alignment.nex-summary.txt: -------------------------------------------------------------------------------- 1 | Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative AT_content GC_content A C G T K M R Y S W B V H D X N O - ? 2 | alignment.nex 90 9150597 823553730 127939673 15.535 6715135 0.734 5359146 0.586 0.508 0.492 192868709 167261641 174996636 160487061 0 1 3 3 1 1 0 1 0 0 0 15940682 0 59625777 52373214 -------------------------------------------------------------------------------- /new_dataset_files/README.md: -------------------------------------------------------------------------------- 1 | How to add a dataset 2 | ==================== 3 | 4 | What you need 5 | ------------- 6 | 7 | 1. A DNA, amino acid, morphology, or language alignment from a published paper. 8 | 9 | 2. A DOI for the dataset, where the dataset is already archived with a CC0 license (this is critical) 10 | 11 | 3. Lots of additional information on the alignment, including: 12 | 13 | (i) Where the loci are (AKA partition boundaries) 14 | 15 | (ii) Which genome (mitochondrial, nuclear, chloroplast) each locus comes from 16 | 17 | (iii) Codon positions (for protein-coding DNA datasets) 18 | 19 | (iv) Ages of sequences (e.g. for aDNA or virus datasets) 20 | 21 | 22 | What you do 23 | ----------- 24 | 25 | 1. Convert your alignment to NEXUS format. The format should be identical to that in Anderson_2013, this is not flexible or negotiable. See below for precise details on how to format this file. 26 | 27 | 2. Add a SETS block to the .nex file with three comments [loci], [genomes], [outgroups]. 28 | 29 | 3. Add CHARSETS that describe each locus to the [loci] section, according to the conventions below. Every site in the alignment needs to be covered by one and only one of these CHARSETS. 30 | 31 | 4. Add CHARSETS that describe each genome of origin to the [genomes] section, according to the conventions below. Every site in the alignment needs to be covered by one and only one of these CHARSETS. 32 | 33 | 5. Define outgroups such that the tree can be rooted. 34 | 35 | 6. If you have heterochronous data, create a SAMPLINGDATES block, and populate it with the sampling dates of all taxa (see Duchene_2015a for an example). 36 | 37 | 7. Check and double check the nexus file. Check it loads into a couple of programs too. 38 | 39 | 7. Make a new folder in the /datasets folder 40 | 41 | 8. Name it after the first author and year of publication (e.g. Brown_2012) 42 | 43 | 9. Copy the README.yaml into the folder. Fill in ALL fields. 44 | 45 | 10. Add in the dataset itself, in NEXUS format, and named alignment.nex 46 | 47 | Running tests and updating the database 48 | --------------------------------------- 49 | 50 | Once your new dataset is in, you need to test the database (including the new dataset), calculate summaries, and update the `summary.csv` file. You will need python 2.7.x and python 3.x. Python scripts are all in the 'python' folder. 51 | 52 | 1. `python check_files.py`. Use Python 2.7.x to check all of the files in your repository, including the new dataset you added. This will run a comprehensive set of tests on all datasets, including checking all of the alignment formats, yaml files, DOI links, etc. 53 | 54 | 2. `python generate_summaries.py`. Use python 3.x to generate summaries of any new datasets (uses AMAS.py, which is included in the repository). 55 | 56 | 3. `python generate_csv.py`. Use python 3.x to generate the summary.csv file. 57 | 58 | On my system, this invovles the following (2.7.x is my default, and I use Conda to manage environments) 59 | 60 | ``` 61 | python check_files.py 62 | source activate snakes 63 | python generate_summaries.py 64 | python generate_csv.py 65 | ``` 66 | 67 | Upload to figshare 68 | ------------------ 69 | 70 | 1. `python gzip_datasets.py` to zip up the datasets 71 | 2. Add any new .tar.gz files to: https://figshare.com/s/622e9e0a156e5233944b 72 | 73 | 74 | Conventions 75 | ----------- 76 | Follow all of these rules... 77 | 78 | 1. Your NEXUS file should start with these two blocks: DATA and SETS. 79 | 80 | 2. It may also contain a SAMPLINGDATES block. 81 | 82 | 3. The DATA block should look like this: 83 | 84 | begin DATA; 85 | dimensions ntax=145 nchar=3037; 86 | format datatype=nucleotide missing=? gap=-; 87 | 88 | The datatype must be either 'nucleotide' or 'protein'. The missing and gap symbols must be as above. 89 | 90 | 4. Your 'SETS' block should look like this before you put the data in: 91 | 92 | begin sets; 93 | 94 | [loci] 95 | 96 | [genomes] 97 | 98 | [outgroups] 99 | 100 | end; 101 | 102 | 5. Inside the 'sets' block, we are aiming for something like this: 103 | 104 | begin SETS; 105 | 106 | [loci] 107 | CHARSET COI_1stpos = 1-1592\3; 108 | CHARSET COI_2ndpos = 2-1592\3; 109 | CHARSET COI_3rdpos = 3-1592\3; 110 | CHARSET 16S = 1593-3037; 111 | 112 | CHARPARTITION loci = 1:COI_1stpos, 113 | 2:COI_2ndpos, 114 | 3:COI_3rdpos, 115 | 4:16S; 116 | 117 | [genomes] 118 | CHARSET mitochondrial_genome = 1-3037; 119 | 120 | CHARPARTITION genomes = 1:mitochondrial_genome; 121 | 122 | [outgroups] 123 | TAXSET outgroups = Afrololigo_mercatoris_FEA Alloteuthis_africana_312327; 124 | 125 | end; 126 | 127 | 6. ALL protein coding genes must have their codon positions delineated. We use the format above, which is e.g. NAME_1stpos. Where "NAME" is the name of the gene. Every gene must have all three positions defined. 128 | 129 | 7. Check that each protein coding gene really is in the frame you think it should be (and that you have indicated in the nexus file). Do this in geneious by translating it and checking the translation by BLASTing the sequence against GenBank and checking the official translation. 130 | 131 | 8. Add information to the genomes section, to make sure that every single base is covered by one of the following annotations: 132 | 133 | mitochondrial_genome 134 | nuclear_genome 135 | chloroplast_genome 136 | dsDNA_genome 137 | ssDNA_genome 138 | dsRNA_genome 139 | ssRNA_genome 140 | 141 | The latter four are reserved for viruses 142 | 143 | 9. If the data is heterochronous (i.e. sampled from multiple time points) make sure that you include a 'SAMPLINGDATES' block. Here's an example: 144 | 145 | begin SAMPLINGDATES; 146 | dimensions ntax=12; 147 | units = calendaryears 148 | FJ174401, 1978 149 | KC990883, 2012 150 | FJ174385, 1961 151 | GQ477151, 2007 152 | HM745325, 2009 153 | HM745346, 2005 154 | JX857503, 2009 155 | HM745344, 2005 156 | HM745350, 2005 157 | FJ174397, 1988 158 | FJ174412, 1993 159 | HM745343, 2005 160 | end; 161 | 162 | 10. In the README.yaml file, fill out everything as instructed in the file itself. Don't change the structure of the yaml file, or delete any entries. 163 | 164 | 11. Fill in the CHARPARTITIONS. Make sure that each CHARPARTITION covers every single base (yes, every single one) in teh alignment. 165 | -------------------------------------------------------------------------------- /new_dataset_files/README.yaml: -------------------------------------------------------------------------------- 1 | study: 2 | reference: [reference taken from Google Scholar, in the VANCOUVER style when you find the paper and press 'cite'] 3 | year: [year of publication, as an integer] 4 | DOI: [URL for the paper starting dx.doi.org, check and double check that this points to the right study] 5 | 6 | dataset: 7 | DOI: [must be a URL for the dataset, starting dx.doi.org, which is different from 'study' DOI, check and double check that this points to the right dataset] 8 | license: [should always == "CC0" or "CCBY", usually Dryad datasets are CC0, and FigShare are CCBY, but you have to know for sure] 9 | used for tree inference: ['yes' or 'no'] 10 | alignment: 11 | ntax: [number of taxa] 12 | nchar: [number of sites] 13 | datatype: [nucleotide or protein] 14 | partitions: [number of partitions] 15 | genomes: 16 | mitochondrial: [yes or no, if it has this genome type] 17 | nuclear: [yes or no, if it has this genome type] 18 | chloroplast: [yes or no, if it has this genome type] 19 | dsDNA: [yes or no, if it has this genome type] 20 | ssDNA: [yes or no, if it has this genome type] 21 | dsRNA: [yes or no, if it has this genome type] 22 | ssRNA: [yes or no, if it has this genome type] 23 | bacterial: [yes or no, if it has this genome type] 24 | timetree root age: ['NA' or an integer followed by 'mya' (millions of year ago); get this from timetree.org, as the age of the root of your tree] 25 | study root age: ['NA' or an integer followed by 'mya' (millions of year ago), if the estimated age of the clade of interest is mentioned in the study itself, put it here] 26 | study clade: 27 | latin: [A single word in latin that describes the smallest clade of organisms that includes all those in the current study] 28 | english: [One or more words] 29 | taxon ID: [a GenBank Taxon ID by searching here: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=, which should be an integer that resolves without a 404 when you add it to the end of this URL: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=, e.g. http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=27563] 30 | notes: ['NA', or some text, for example if the dataset DOI points to lots of datasets, we need to know which one we have here, or if you need to provide information about which of many datasets you used, etc.] 31 | -------------------------------------------------------------------------------- /utility_scripts/README.md: -------------------------------------------------------------------------------- 1 | 2 | 3 | # Basic procedure when adding a dataset 4 | 5 | ``` 6 | # check files (Python 2.7.x) 7 | python check_files.py 8 | 9 | # make summaries (Python 3.x) 10 | source activate snakes 11 | python generate_summaries.py 12 | 13 | # update csv 14 | python generate_csv.py 15 | 16 | # zip up the datasets 17 | source deactivate 18 | python gzip_datasets.py 19 | 20 | 21 | ``` -------------------------------------------------------------------------------- /utility_scripts/charpartition_generator.py: -------------------------------------------------------------------------------- 1 | # a little script to generate charpartitions from files of charsets 2 | filename = "/Users/roblanfear/Desktop/sets.txt" 3 | 4 | charsets = open(filename, 'r').readlines() 5 | 6 | names = [s.split("=")[0].split("CHARSET")[1].strip() for s in charsets] 7 | 8 | parts = [] 9 | for i, n in enumerate(names): 10 | print i, n 11 | part = ''.join([str(i+1), ":", n, ","]) 12 | parts.append(part) 13 | 14 | charpartition = ' '.join(parts) 15 | charpartition = charpartition.rstrip(",") 16 | 17 | charpartition = ''.join([charpartition, ";"]) 18 | 19 | print charpartition -------------------------------------------------------------------------------- /utility_scripts/check_files.py: -------------------------------------------------------------------------------- 1 | # performs basic checks on the DB, and builds a CSV file ... 2 | 3 | import os 4 | import logging 5 | import csv 6 | import glob 7 | from util_functions import * 8 | 9 | 10 | 11 | 12 | logging.basicConfig(format='%(levelname)s:\t%(asctime)s:\t%(message)s', datefmt='%m/%d/%Y %I:%M:%S %p', level=logging.DEBUG) 13 | 14 | # first we get a list of all the datasets 15 | # each one is a dataset that SHOULD have an associated .yaml readme 16 | dataset_folders = [x[0] for x in walklevel(os.path.join(os.getcwd(), "../datasets"))][1:] 17 | 18 | logging.info("Found %d datasets" %(len(dataset_folders))) 19 | for f in dataset_folders: 20 | logging.info(" %s", f) 21 | 22 | # read each file and extract the things you want, writing a csv as you go 23 | warnings = 0 24 | 25 | for folder in dataset_folders: 26 | 27 | folder = os.path.realpath(folder) # prettier 28 | logging.info("Checking %s" %folder) 29 | 30 | # 1. Check that the two files exist, at least in principle (maybe they're empty) 31 | files = os.listdir(folder) 32 | if files.count("README.yaml") != 1: 33 | logging.error("couldn't find a YAML file for %s" %folder) 34 | raise ValueError 35 | logging.info(" found YAML file") 36 | 37 | if files.count("alignment.nex") != 1: 38 | logging.error("couldn't find alignment.nex file for %s" %folder) 39 | raise ValueError 40 | 41 | logging.info(" found alignment.nex file") 42 | 43 | # clean up the folder: remove all files except the two we want 44 | extras = set(files) - set(['alignment.nex', 'README.yaml', 'alignment.nex-seq-summary.txt', 'alignment.nex-summary.txt']) 45 | if extras: 46 | logging.info(" removing %d additional file(s)", len(extras)) 47 | for f in extras: 48 | logging.info(" %s" %(f)) 49 | os.remove(os.path.join(folder, f)) 50 | 51 | # 2. parse the yaml file 52 | logging.info(" checking YAML file") 53 | yaml_file = os.path.join(folder, "README.yaml") 54 | check_yaml(yaml_file) 55 | 56 | # 4. check the alignment file 57 | logging.info(" checking alignment.nex file") 58 | 59 | alignment_file = os.path.join(folder, "alignment.nex") 60 | aln = check_alignment(alignment_file) 61 | 62 | logging.info(" done, no errors found") 63 | 64 | logging.info("Database contains %d datasets" % ( len(dataset_folders))) 65 | logging.info("All datasets checked and no errors detected") 66 | 67 | -------------------------------------------------------------------------------- /utility_scripts/concatenate_loci.py: -------------------------------------------------------------------------------- 1 | # a little script to concatenate lots of nexus files in a folder 2 | # and write a new one. 3 | # cd to the infile before running 4 | 5 | from Bio.Nexus import Nexus 6 | from Bio import AlignIO 7 | import os 8 | 9 | infile = "/Users/roblanfear/Dropbox/Projects_Current/benchmark_alignments_in_progress/Wu_2018_aa/cds_aa_nex" 10 | 11 | file_list = [x for x in os.walk(infile)][0][2] 12 | print(file_list) 13 | 14 | try: 15 | file_list.remove(".DS_Store") # thanks Mac 16 | except: 17 | pass 18 | 19 | print("loading files") 20 | nexi = [(fname, Nexus.Nexus(fname)) for fname in file_list] 21 | 22 | print("combining alignments") 23 | combined = Nexus.combine(nexi) 24 | 25 | print("writing output") 26 | outfile = os.path.join(infile, "alignment.nex") 27 | outfile = open(outfile, 'w') 28 | combined.write_nexus_data(outfile) 29 | outfile.close() -------------------------------------------------------------------------------- /utility_scripts/convert_to_nexus.py: -------------------------------------------------------------------------------- 1 | # convert a file full of alignments to nexus format 2 | # just change the input format in the loop as appropriate 3 | # and the alphabet 4 | 5 | from Bio.Alphabet import generic_protein 6 | from Bio import AlignIO 7 | import os 8 | 9 | infile = "/Users/roblanfear/Dropbox/Projects_Current/benchmark_alignments_in_progress/Wu_2018_aa/cds_aa" 10 | outdir = "/Users/roblanfear/Dropbox/Projects_Current/benchmark_alignments_in_progress/Wu_2018_aa/cds_aa_nex" 11 | 12 | file_list = [x for x in os.walk(infile)][0][2] 13 | 14 | try: 15 | file_list.remove(".DS_Store") # thanks Mac 16 | except: 17 | pass 18 | 19 | for f in file_list: 20 | print(f) 21 | a = AlignIO.read(open(os.path.join(infile, f)), "phylip") 22 | a._alphabet = generic_protein 23 | 24 | name = os.path.basename(f) 25 | outfile = os.path.join(outdir, name) 26 | 27 | AlignIO.write(a, outfile, "nexus") -------------------------------------------------------------------------------- /utility_scripts/generate_csv.py: -------------------------------------------------------------------------------- 1 | #!python3.5 2 | import os 3 | import yaml 4 | import pandas as pd 5 | import glob 6 | import AMAS 7 | 8 | # generate a csv from the YAML files 9 | all_files = glob.glob(os.path.abspath(os.path.join(os.getcwd(),'../datasets/**/*.yaml')), recursive=True) 10 | df_from_each_yaml = (pd.io.json.json_normalize(yaml.load(open(f))) for f in all_files) 11 | concatenated_yaml = pd.concat(df_from_each_yaml, ignore_index=True) 12 | 13 | # get summaries as df 14 | all_smys_f = glob.glob(os.path.abspath(os.path.join(os.getcwd(),'../datasets/**/alignment.nex-summary.txt')), recursive=True) 15 | all_smys = (pd.read_table(open(f)) for f in all_smys_f) 16 | concatenated_smy = pd.concat(all_smys, ignore_index=True, axis=0) 17 | 18 | cols = ['Total_matrix_cells', 19 | 'Undetermined_characters', 20 | 'Missing_percent', 21 | 'No_variable_sites', 22 | 'Proportion_variable_sites', 23 | 'Parsimony_informative_sites', 24 | 'Proportion_parsimony_informative', 25 | 'AT_content', 26 | 'GC_content'] 27 | 28 | concatenated_smy = concatenated_smy[cols] 29 | 30 | # get data types 31 | 32 | 33 | 34 | # dataset names 35 | datasets = glob.glob(os.path.abspath(os.path.join(os.getcwd(),'../datasets/*'))) 36 | datasets = [os.path.basename(f) for f in datasets] 37 | concatenated_smy.insert(0, 'name', datasets) 38 | concatenated_yaml.insert(0, 'name', datasets) 39 | 40 | # merge 41 | summarydf = pd.merge(concatenated_smy, concatenated_yaml, how='left', left_on=['name'], right_on = ['name']) 42 | 43 | # write 44 | summarydf.to_csv(os.path.abspath(os.path.join(os.getcwd(),'../summary.csv'))) 45 | 46 | -------------------------------------------------------------------------------- /utility_scripts/generate_summaries.py: -------------------------------------------------------------------------------- 1 | # generates AMAS summaries for all datasets, only where they are missing 2 | 3 | import AMAS 4 | from Bio.Nexus import Nexus 5 | import os 6 | import glob 7 | 8 | cores = 4 9 | 10 | all_files = glob.glob(os.path.abspath(os.path.join(os.getcwd(),'..','datasets','**')), recursive=False) 11 | 12 | print(all_files) 13 | 14 | for f in all_files: 15 | alnf = os.path.join(f, 'alignment.nex') 16 | 17 | print(alnf) 18 | 19 | sumf = os.path.join(f, "alignment.nex-summary.txt") 20 | taxf = os.path.join(f, "alignment.nex-seq-summary.txt") 21 | 22 | if os.path.isfile(sumf)==True and os.path.isfile(taxf)==True: 23 | pass 24 | else: 25 | # get the data type 26 | dat = Nexus.Nexus() 27 | dat.read(alnf) 28 | if(dat.datatype=='nucleotide'): type = 'dna' 29 | if(dat.datatype=='protein'): type= 'aa' 30 | 31 | # get the AMAS summaries 32 | aln = AMAS.MetaAlignment(in_files=[alnf], data_type=type,in_format="nexus", cores=cores) 33 | aln.write_summaries(sumf) 34 | aln.write_taxa_summaries() 35 | 36 | -------------------------------------------------------------------------------- /utility_scripts/gzip_datasets.py: -------------------------------------------------------------------------------- 1 | import os 2 | from util_functions import * 3 | 4 | # first we get a list of all the datasets 5 | dataset_folders = [x[0] for x in walklevel(os.path.join(os.getcwd(), "../datasets"))][1:] 6 | 7 | os.mkdir("../zips/") 8 | 9 | for f in dataset_folders: 10 | b = os.path.basename(f) 11 | command = "tar -zcvf ../zips/%s.tar.gz -C ../datasets/ %s" %(b, b) 12 | print(command) 13 | os.system(command) -------------------------------------------------------------------------------- /utility_scripts/split_files.sh: -------------------------------------------------------------------------------- 1 | # to split a big file 2 | f="/Users/roblanfear/Documents/github/BenchmarkAlignments/possible_datasets/Wu_2018/alignment.nex" 3 | 4 | split -b 50m $f $f'.' 5 | 6 | # to join files back into a single alignment 7 | d="/Users/roblanfear/Documents/github/BenchmarkAlignments/possible_datasets/Wu_2018/" 8 | cat $d"alignment.nex."* > $d"alignment.nex" -------------------------------------------------------------------------------- /utility_scripts/split_into_loci.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | 3 | # recursively find all benchmark alignment files and output information on individual loci 4 | from Bio.Nexus import Nexus 5 | import glob 6 | import os 7 | from argparse import ArgumentParser 8 | 9 | parser = ArgumentParser() 10 | parser.add_argument("-i", "--infolder", dest="infolder", 11 | help="input file - input folder alignment from Benchmark Alignments database") 12 | 13 | parser.add_argument("-o", "--outfolder", dest="outfolder", 14 | help="output folder - existing folder to which to ouput single-locus alignments. Note that ") 15 | 16 | args = parser.parse_args() 17 | 18 | 19 | print(args) 20 | 21 | alignments = glob.glob(os.path.join(args.infolder, '**', '*.nex'), recursive=True) 22 | 23 | try: 24 | os.mkdir(args.outfolder) 25 | print("Directory ", args.outfolder, "created") 26 | except FileExistsError: 27 | print("Directory ", args.outfolder, " already exists") 28 | 29 | for infile in alignments: 30 | 31 | print("Extracting loci from ", infile) 32 | 33 | aln = Nexus.Nexus() 34 | 35 | aln.read(infile) 36 | 37 | # first we get everything except the genomes 38 | all_charsets = list(aln.charsets.keys()) 39 | 40 | # delete genome charsets 41 | charsets = list(filter(lambda x:'genome' not in x, all_charsets)) 42 | 43 | # merge all loci with 1st, 2nd, and 3rd sites 44 | endings = ["_1stpos", "_2ndpos", "_3rdpos"] 45 | loci = {} 46 | for c in charsets: 47 | 48 | # a key for the locus dict 49 | key = c 50 | # the sites for this key 51 | c_sites = aln.charsets[key] 52 | 53 | for e in endings: 54 | if c.endswith(e): 55 | new_key = c[:-len(e)] 56 | break 57 | else: 58 | new_key = key 59 | 60 | # add the sites to any existing sites for that locus 61 | all_sites = loci.setdefault(new_key, []) 62 | all_sites += c_sites 63 | loci[new_key] = all_sites 64 | 65 | aln_folder = os.path.basename(os.path.dirname(infile)) 66 | 67 | # prepend the alignment name to the output files 68 | out_path = os.path.join(args.outfolder, aln_folder) 69 | 70 | # output loci 71 | aln.write_nexus_data_partitions(filename=out_path, charpartition=loci) -------------------------------------------------------------------------------- /utility_scripts/translate_alignments.py: -------------------------------------------------------------------------------- 1 | # translate a bunch of alignments 2 | # cd to the folder with the alignments to be translated first 3 | 4 | import os 5 | 6 | # input file, can't be NEXUS alignments 7 | infile = "/Users/roblanfear/Dropbox/Projects_Current/benchmark_alignments_in_progress/Wu_2018_aa/cds_aa" 8 | outdir = "/Users/roblanfear/Dropbox/Projects_Current/benchmark_alignments_in_progress/Wu_2018_aa/cds_aa_nex" 9 | 10 | file_list = [x for x in os.walk(infile)][0][2] 11 | 12 | try: 13 | file_list.remove(".DS_Store") # thanks Mac 14 | except: 15 | pass 16 | 17 | for f in file_list: 18 | print(f) 19 | 20 | name = os.path.basename(f) 21 | outfile = os.path.join(outdir, name) 22 | 23 | print(name, outfile) 24 | 25 | cmd = "~/Desktop/iqtree -st NT2AA -s %s -ao %s" %(name, outfile) 26 | 27 | os.system(cmd) --------------------------------------------------------------------------------