├── .gitignore ├── .gitmodules ├── README.md ├── clamsa.py ├── data ├── download_fly_vert_yeast_train.sh ├── download_vert_test.sh ├── train_dNdS │ ├── amniota-test-m0.tfrecord.gz │ ├── amniota-train-m0.tfrecord.gz │ └── amniota-val-m0.tfrecord.gz └── train_dNdS_class │ ├── amniota-test-m0.tfrecord.gz │ ├── amniota-train-m0.tfrecord.gz │ └── amniota-val-m0.tfrecord.gz ├── docs ├── conversion.md ├── usage-predict-sitewise.md ├── usage-predict.md └── usage-train.md ├── examples ├── amniota.nwk ├── coding_sitewise │ ├── TLCD3A-diverse64.maf │ ├── TLCD3A-region.png │ ├── diverse64.nwk │ └── expected_output │ │ ├── coding_sitewise.track │ │ ├── coding_sitewise0.wig │ │ ├── coding_sitewise1.wig │ │ ├── coding_sitewise2.wig │ │ ├── coding_sitewise3.wig │ │ ├── coding_sitewise4.wig │ │ └── coding_sitewise5.wig ├── dNdS_alignments │ ├── 11.fa │ ├── 12.fa │ ├── 13.fa │ ├── 14.fa │ ├── 15.fa │ ├── 16.fa │ ├── 17.fa │ ├── 18.fa │ ├── 19.fa │ └── 20.fa ├── dNdS_class_alignments │ ├── 11.fa │ ├── 12.fa │ ├── 13.fa │ ├── 14.fa │ ├── 15.fa │ ├── 16.fa │ ├── 17.fa │ ├── 18.fa │ ├── 19.fa │ └── 20.fa ├── example_tree.nwk ├── example_tree.png ├── fly.nwk ├── msa.lst ├── msa1-2.png ├── msa1.fa ├── msa2.fa ├── vertebrate.nwk └── yeast.nwk ├── matrices ├── external-use-of-rate-matrices.pdf └── vert-fly-yeast-LogReg-M3 │ ├── Theta.txt │ ├── rates-Q.txt │ └── rates-pi.txt ├── models ├── __init__.py ├── tcmc_dNdS.py ├── tcmc_dNdS_class.py ├── tcmc_mean_log.py ├── tcmc_rnn.py └── test.py ├── saved_weights ├── diverse64mammals │ └── tcmc_dNdS_class │ │ ├── 2023.11.27--15.07.07.h5 │ │ ├── 2024.02.26--08.51.09.h5 │ │ ├── mammals-sitewise.h5 │ │ └── mammals-sitewise │ │ └── events.out.tfevents.1701097627.apphub-stankem-549dddf8f5-nqh6k.131.695.v2 ├── drosophilidae_amniota │ ├── tcmc_dNdS │ │ ├── 2023.09.18--11.29.27.h5 │ │ └── 2023.09.18--11.29.27 │ │ │ ├── events.out.tfevents.1695036567.apphub-s-dameis-9f7c6c9cf-cdx5v.285.1.v2 │ │ │ ├── test │ │ │ └── events.out.tfevents.1695040597.apphub-s-dameis-9f7c6c9cf-cdx5v.285.4.v2 │ │ │ ├── train │ │ │ └── events.out.tfevents.1695036568.apphub-s-dameis-9f7c6c9cf-cdx5v.285.2.v2 │ │ │ └── validation │ │ │ └── events.out.tfevents.1695036597.apphub-s-dameis-9f7c6c9cf-cdx5v.285.3.v2 │ └── tcmc_dNdS_class │ │ ├── 2023.09.21--12.07.25.h5 │ │ └── 2023.09.21--12.07.25 │ │ ├── events.out.tfevents.1695298045.apphub-s-dameis-9f7c6c9cf-xbsrg.15024.1.v2 │ │ ├── test │ │ └── events.out.tfevents.1695302716.apphub-s-dameis-9f7c6c9cf-xbsrg.15024.4.v2 │ │ ├── train │ │ └── events.out.tfevents.1695298046.apphub-s-dameis-9f7c6c9cf-xbsrg.15024.2.v2 │ │ └── validation │ │ └── events.out.tfevents.1695298078.apphub-s-dameis-9f7c6c9cf-xbsrg.15024.3.v2 ├── fly │ └── tcmc_rnn │ │ ├── 2021.10.23--10.22.35.h5 │ │ ├── fly-gruM8.h5 │ │ └── fly-gruM8 │ │ └── events.out.tfevents.1634977355.greif1.189902.26.v2 ├── fly_vertebrate_yeast │ └── tcmc_rnn │ │ ├── 2021.01.04--05.47.56.h5 │ │ ├── 2021.10.26--12.06.19.h5 │ │ ├── default.h5 │ │ └── default │ │ └── events.out.tfevents.1609735676.greif1.123468.582738.v2 └── vertebrate │ └── tcmc_rnn │ ├── 2021.10.17--07.47.25.h5 │ ├── vert-gruM8.h5 │ └── vert-gruM8 │ └── events.out.tfevents.1634449645.greif1.59758.42.v2 ├── test ├── amniota_class_data.lst ├── amniota_data.lst ├── clamsa_vert.csv ├── convert.sh ├── convert_dNdS.bash ├── convert_dNdS_class.bash ├── predict.sh ├── predict_dNdS.bash ├── predict_dNdS_class.bash ├── train.sh ├── train_dNdS.bash ├── train_dNdS_class.bash └── vertebrate.test.msa.lst └── utilities ├── __init__.py ├── coding-labeled-MSAs.py ├── database_reader.py ├── maf-split.pl ├── make_all_wig_tracks.sh ├── make_wig_track.sh ├── model_evaluation.py ├── msa_converter.py ├── newick_parser.py ├── onehot_tuple_encoder.py ├── training.py ├── visualization.py └── wiggle.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gaius-Augustus/clamsa/HEAD/.gitignore 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