├── .gitignore ├── CMakeLists.txt ├── LICENSE.md ├── README.rst ├── azure-pipelines.yml ├── example ├── galGal6_chr22_25_28_each_30k_bases.maf.gz ├── galGal6_chr22_25_28_subset_ensGene.gtf ├── galGal6_chr22_25_28_subset_ncbiRefSeq.gtf ├── galGal6_chr22_25_28_subset_refGene.gtf ├── galGal6_coding_exons.txt └── tracks │ ├── PhyloCSF+1.bw │ ├── PhyloCSF+2.bw │ ├── PhyloCSF+3.bw │ ├── PhyloCSF-1.bw │ ├── PhyloCSF-2.bw │ ├── PhyloCSF-3.bw │ └── PhyloCSFpower.bw ├── src ├── additional_scores.hpp ├── arg_parse.hpp ├── bitvector.hpp ├── common.hpp ├── create_tracks.hpp ├── ecm.hpp ├── estimate_hmm_parameter.hpp ├── fixed_lik.hpp ├── gff_reader.hpp ├── instance.hpp ├── models.hpp ├── newick.hpp ├── omega.hpp ├── parallel_file_reader.hpp ├── phylocsf++.cpp ├── phylocsf++annotate_with_mmseqs.hpp ├── phylocsf++annotate_with_tracks.hpp ├── phylocsf++build_tracks.hpp ├── phylocsf++find_cds.hpp ├── phylocsf++score_msa.hpp ├── run.hpp ├── translation.hpp └── wig_file_reader.hpp └── test ├── 53birds.nh ├── 53birds_coding.ECM ├── 53birds_noncoding.ECM ├── automatic_tests.cpp ├── expected_results ├── annotate-with-tracks │ ├── galGal6_chr22_25_28_subset_ensGene.PhyloCSF++.gtf │ ├── galGal6_chr22_25_28_subset_ncbiRefSeq.PhyloCSF++.gtf │ └── galGal6_chr22_25_28_subset_refGene.PhyloCSF++.gtf └── build-tracks │ ├── PhyloCSF+1.wig │ ├── PhyloCSF+2.wig │ ├── PhyloCSF+3.wig │ ├── PhyloCSF-1.wig │ ├── PhyloCSF-2.wig │ ├── PhyloCSF-3.wig │ ├── PhyloCSFRaw+1.wig │ ├── PhyloCSFRaw+2.wig │ ├── PhyloCSFRaw+3.wig │ ├── PhyloCSFRaw-1.wig │ ├── PhyloCSFRaw-2.wig │ ├── PhyloCSFRaw-3.wig │ └── PhyloCSFpower.wig ├── maf-file-medium ├── PhyloCSF-results │ ├── chr22.516alignments.PhyloCSF.fixed.scores │ ├── chr22.516alignments.PhyloCSF.mle.scores │ └── chr22.516alignments.PhyloCSF.omega.scores ├── chr22.516alignments.maf ├── chr22.516alignments.maf.fixed.scores ├── chr22.516alignments.maf.mle.scores ├── chr22.516alignments.maf.omega.scores └── chr22.head.orig.results.formatted ├── maf-file-small ├── 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