bin/convert_orthofinder_tree_ids.py
bin/create_files_for_hogs.py
bin/make_ultrametric.py
bin/orthofinder
bin/orthogroup_gene_count.py
bin/primary_transcript.py
bin/src/orthofinder/__init__.py
bin/src/orthofinder/_version.py
bin/src/orthofinder/citation.py
bin/src/orthofinder/comparative_genomics/__init__.py
bin/src/orthofinder/comparative_genomics/orthologues.py
bin/src/orthofinder/comparative_genomics/stats.py
bin/src/orthofinder/file_updates/__init__.py
bin/src/orthofinder/file_updates/file_updates.py
bin/src/orthofinder/file_updates/ogs.py
bin/src/orthofinder/file_updates/trees.py
bin/src/orthofinder/gene_tree_inference/__init__.py
bin/src/orthofinder/gene_tree_inference/infer_trees.py
bin/src/orthofinder/gene_tree_inference/resolve.py
bin/src/orthofinder/gene_tree_inference/trees2ologs_of.py
bin/src/orthofinder/orthogroups/__init__.py
bin/src/orthofinder/orthogroups/accelerate.py
bin/src/orthofinder/orthogroups/gathering.py
bin/src/orthofinder/orthogroups/orthogroups_set.py
bin/src/orthofinder/orthogroups/sample_genes.py
bin/src/orthofinder/run/__init__.py
bin/src/orthofinder/run/__main__.py
bin/src/orthofinder/run/check_dependencies.py
bin/src/orthofinder/run/config.json
bin/src/orthofinder/run/helpinfo.py
bin/src/orthofinder/run/process_args.py
bin/src/orthofinder/run/run_commands.py
bin/src/orthofinder/run/run_info.py
bin/src/orthofinder/run/species_info.py
bin/src/orthofinder/tools/__init__.py
bin/src/orthofinder/tools/astral.py
bin/src/orthofinder/tools/consensus_tree.py
bin/src/orthofinder/tools/dendroblast.py
bin/src/orthofinder/tools/mcl.py
bin/src/orthofinder/tools/newick.py
bin/src/orthofinder/tools/stag.py
bin/src/orthofinder/tools/stride.py
bin/src/orthofinder/tools/tree.py
bin/src/orthofinder/tools/trees_msa.py
bin/src/orthofinder/tools/trim.py
bin/src/orthofinder/tools/waterfall.py
bin/src/orthofinder/utils/__init__.py
bin/src/orthofinder/utils/blast_file_processor.py
bin/src/orthofinder/utils/fasta_processor.py
bin/src/orthofinder/utils/files.py
bin/src/orthofinder/utils/matrices.py
bin/src/orthofinder/utils/parallel_task_manager.py
bin/src/orthofinder/utils/program_caller.py
bin/src/orthofinder/utils/split_ortholog_files.py
bin/src/orthofinder/utils/util.py
share/orthofinder/ExampleData/AdditionalSpecies/M_arthritidis.fa
share/orthofinder/ExampleData/AdditionalSpecies/M_haemocanis.fa
share/orthofinder/ExampleData/Mycoplasma_agalactiae.faa
share/orthofinder/ExampleData/Mycoplasma_gallisepticum.faa
share/orthofinder/ExampleData/Mycoplasma_genitalium.faa
share/orthofinder/ExampleData/Mycoplasma_hyopneumoniae.faa
