├── .gitignore ├── .gitmodules ├── LICENSE ├── Makefile ├── PartitionFinder.py ├── PartitionFinderMorphology.py ├── PartitionFinderProtein.py ├── README.md ├── clean_tests.sh ├── docs ├── Manual_v2.1.x.docx ├── Manual_v2.1.x.pdf ├── PartitionFinder2的一般使用方法（中文版-网页版）.html ├── citationsplot.pdf ├── citationsplot2.pdf ├── downloadplot.r ├── downloadplot_combined.pdf ├── downloadplot_v1.pdf └── downloadstats.csv ├── examples ├── README.txt ├── aminoacid │ ├── partition_finder.cfg │ └── test.phy ├── morphology │ ├── partition_finder.cfg │ └── test.phy └── nucleotide │ ├── partition_finder.cfg │ └── test.phy ├── partfinder ├── __init__.py ├── algorithm.py ├── alignment.py ├── analysis.py ├── analysis_method.py ├── config.py ├── database.py ├── dependencies.py ├── entropy.py ├── kmeans.py ├── logtools.py ├── main.py ├── model_loader.py ├── model_utils.py ├── models.csv ├── morph_tiger.py ├── neighbour.py ├── parser.py ├── phyml.py ├── phyml_models.py ├── progress.py ├── raxml.py ├── raxml_models.py ├── reporter.py ├── results.py ├── scheme.py ├── submodels.py ├── subset.py ├── subset_ops.py ├── threadpool.py └── util.py ├── programs ├── README.md ├── phyml ├── phyml.exe ├── phyml.linux ├── raxml ├── raxml.exe ├── raxml.linux ├── raxml_pthreads ├── raxml_pthreads.exe └── raxml_pthreads.linux ├── tests ├── PF2 │ ├── __init__.py │ ├── missing-sites-warning │ │ ├── Als_etal_2004.phy │ │ └── partition_finder.cfg │ ├── overlapping-blocks │ │ ├── Als_etal_2004.phy │ │ └── partition_finder.cfg │ └── test_pf2.py ├── __init__.py ├── all_succeed │ ├── 1subset │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── __init__.py │ └── test_all_success.py ├── cfg │ ├── __init__.py │ ├── test01.cfg │ ├── test02.cfg │ ├── test03.cfg │ ├── test04.cfg │ ├── test05.cfg │ ├── test06.cfg │ ├── test07.cfg │ ├── test08.cfg │ ├── test09.cfg │ ├── test10.cfg │ ├── test11.cfg │ ├── test12.cfg │ ├── test13.cfg │ ├── test14.cfg │ ├── test15.cfg │ ├── test16.cfg │ └── test_configs.py ├── christof │ ├── __init__.py │ ├── alignment-error │ │ ├── Als_etal_2004.phy │ │ └── partition_finder.cfg │ ├── clustering-phyml-dna │ │ ├── partition_finder.cfg │ │ └── test.phy │ ├── clustering-raxml-dna │ │ ├── partition_finder.cfg │ │ └── test.phy │ ├── greedy-phyml-dna │ │ ├── partition_finder.cfg │ │ └── test.phy │ ├── greedy-phyml-protein │ │ ├── Als_etal_2004.phy │ │ └── partition_finder.cfg │ ├── greedy-raxml-dna │ │ ├── partition_finder.cfg │ │ └── test.phy │ ├── greedy-raxml-protein │ │ ├── Als_etal_2004.phy │ │ └── partition_finder.cfg │ ├── model-greedy-phyml01 │ │ ├── Als_etal_2004.phy │ │ └── partition_finder.cfg │ ├── model-greedy-phyml02 │ │ ├── Als_etal_2004.phy │ │ └── partition_finder.cfg │ ├── model-greedy-phyml03 │ │ ├── Als_etal_2004.phy │ │ └── partition_finder.cfg │ ├── model-greedy-raxml01 │ │ ├── Als_etal_2004.phy │ │ └── partition_finder.cfg │ ├── model-greedy-raxml02 │ │ ├── Als_etal_2004.phy │ │ └── partition_finder.cfg │ ├── model-greedy-raxml03 │ │ ├── Als_etal_2004.phy │ │ └── partition_finder.cfg │ ├── overlap-error │ │ ├── Als_etal_2004.phy │ │ └── partition_finder.cfg │ └── test_christof.py ├── clustering │ ├── DNA_hcluster1 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_hcluster2 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_hcluster3 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_hcluster4 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_hcluster5 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_hcluster6 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_hcluster7 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_rcluster1 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_rcluster10 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_rcluster11 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_rcluster12 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_rcluster13 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_rcluster14 │ │ ├── alignment.phy │ │ ├── cmdline.txt │ │ └── partition_finder.cfg │ ├── DNA_rcluster2 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_rcluster3 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_rcluster4 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_rcluster5 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_rcluster6 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_rcluster7 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_rcluster8 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA_rcluster9 │ │ ├── Caterino_2001.phy │ │ ├── cmdline.txt │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── __init__.py │ ├── prot_hcluster1 │ │ ├── cmdline.txt │ │ ├── concat_alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── prot_hcluster2 │ │ ├── cmdline.txt │ │ ├── concat_alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── prot_hcluster3 │ │ ├── cmdline.txt │ │ ├── concat_alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── prot_rcluster1 │ │ ├── cmdline.txt │ │ ├── concat_alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── prot_rcluster2 │ │ ├── cmdline.txt │ │ ├── concat_alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── prot_rcluster3 │ │ ├── cmdline.txt │ │ ├── concat_alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── prot_rcluster4 │ │ ├── cmdline.txt │ │ ├── concat_alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── prot_rcluster5 │ │ ├── cmdline.txt │ │ ├── concat_alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── test_clustering.py │ └── tests.txt ├── full_analysis │ ├── DNA1 │ │ ├── Caterino_2001.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA2 │ │ ├── Caterino_2001.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA3-analysis.zip │ ├── DNA3 │ │ ├── Caterino_2001.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA4 │ │ ├── Caterino_2001.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA5 │ │ ├── Caterino_2001.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA6 │ │ ├── Caterino_2001.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA7 │ │ ├── Caterino_2001.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── DNA8 │ │ ├── Caterino_2001.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── __init__.py │ ├── kmeans1 │ │ ├── alignment.phy │ │ └── partition_finder.cfg │ ├── kmeans_fast │ │ ├── alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── prot1 │ │ ├── concat_alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── prot2 │ │ ├── concat_alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── prot3 │ │ ├── concat_alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── prot4 │ │ ├── concat_alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── prot5 │ │ ├── concat_alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── prot6 │ │ ├── concat_alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── prot7 │ │ ├── concat_alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── prot8 │ │ ├── concat_alignment.phy │ │ ├── partition_finder.cfg │ │ └── results.bin │ ├── rerun01 │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── rerun02 │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── rerun03 │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── rerun04 │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── rerun05 │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── rerun06 │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── rerun07 │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── rerun08 │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── rerun09 │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── rerun10 │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── rerun11 │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── rerun12 │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── rerun13 │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── rerun14 │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── rerun15 │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── rerun20 │ │ ├── Caterino_2001.phy │ │ └── partition_finder.cfg │ ├── rerun21 │ │ ├── Caterino_2001.phy │ │ ├── DNA3-analysis.zip │ │ └── partition_finder.cfg │ ├── test_full.py │ └── tests.txt ├── kmeans │ ├── Grande_2013 │ │ ├── README.yaml │ │ ├── alignment.phy │ │ └── partition_finder.cfg │ ├── __init__.py │ ├── fabrications1 │ │ ├── README.yaml │ │ ├── alignment.phy │ │ └── partition_finder.cfg │ ├── fabrications2 │ │ ├── README.yaml │ │ ├── alignment.phy │ │ └── partition_finder.cfg │ └── test_kmeans.py ├── kmeans_ml_tree │ ├── DNA_entropy │ │ ├── partition_finder.cfg │ │ └── test.phy │ ├── DNA_tiger │ │ ├── partition_finder.cfg │ │ └── test.phy │ ├── __init__.py │ ├── morph_entropy │ │ ├── partition_finder.cfg │ │ └── single_column.phy │ ├── morph_tiger │ │ ├── partition_finder.cfg │ │ └── single_column.phy │ └── test_ml_tree.py ├── misc │ ├── Caterino_2001.phy │ ├── interleave.phy │ ├── raxml_aminoacid.output │ ├── raxml_aminoacid_LG4M+G.output │ └── raxml_nucleotide.output ├── morphology │ ├── __init__.py │ ├── aicctest │ │ ├── partition_finder.cfg │ │ └── single_column.phy │ ├── aictest │ │ ├── partition_finder.cfg │ │ └── single_column.phy │ ├── bictest │ │ ├── partition_finder.cfg │ │ └── single_column.phy │ ├── binASC │ │ ├── partition_finder.cfg │ │ └── single_column.phy │ ├── bin_wrongdata │ │ ├── partition_finder.cfg │ │ └── single_column.phy │ ├── binary │ │ ├── partition_finder.cfg │ │ └── single_column.phy │ ├── incmat │ │ ├── partition_finder.cfg │ │ └── single_column.phy │ ├── modeltest │ │ ├── partition_finder.cfg │ │ └── single_column.phy │ ├── multiASC │ │ ├── partition_finder.cfg │ │ └── single_column.phy │ ├── multistate │ │ ├── partition_finder.cfg │ │ └── single_column.phy │ ├── test_AIC.py │ ├── test_aicc.py │ ├── test_bic.py │ ├── test_incorrectmat.py │ ├── test_mat.py │ ├── test_modelBin.py │ ├── test_modelBinASC.py │ ├── test_modelBinMisSpec.py │ ├── test_modelMulti.py │ ├── test_modelMultiASC.py │ ├── test_modeloutput.py │ ├── test_nsubs.py │ ├── test_wrongmodel.py │ ├── tiger │ │ ├── test_parse_to_rates.py │ │ └── test_rate_calc.py │ └── wrongmodel │ │ ├── partition_finder.cfg │ │ └── single_column.phy ├── nuc_single_site │ ├── partition_finder.cfg │ └── single_site.phy ├── paul │ ├── RAxML_perSiteLLs.testing │ ├── __init__.py │ ├── fabricated │ │ ├── fabricated.phy │ │ └── partition_finder.cfg │ ├── free_rates_4_cat.phy_phyml_lk.txt │ ├── gamma_8_cat.phy_phyml_lk.txt │ └── simulated_TRUE.phy_phyml_lk.txt ├── quick_analysis │ ├── __init__.py │ ├── all │ │ ├── partition_finder.cfg │ │ └── random.phy │ ├── aln_RY │ │ ├── partition_finder.cfg │ │ └── random.phy │ ├── aln_interleaved │ │ ├── partition_finder.cfg │ │ └── random.phy │ ├── greedy │ │ ├── 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