LICENSE
README.md
setup.cfg
setup.py
bin/run-raxml
bin/setup-generax
topiary/__init__.py
topiary/__version__.py
topiary/_private.py
topiary/check/__init__.py
topiary/check/paralog_patterns.py
topiary/check/standard.py
topiary/check/topiary_dataframe.py
topiary/draw/__init__.py
topiary/draw/_base.py
topiary/draw/ancestor.py
topiary/draw/ml.py
topiary/draw/reconciliation.py
topiary/draw/species.py
topiary/draw/tree.py
topiary/external/__init__.py
topiary/external/_interface.py
topiary/external/muscle.py
topiary/external/generax/__init__.py
topiary/external/generax/_generax.py
topiary/external/generax/reconcile.py
topiary/external/ncbi/__init__.py
topiary/external/ncbi/_parse_ncbi_line.py
topiary/external/ncbi/blast/__init__.py
topiary/external/ncbi/blast/local.py
topiary/external/ncbi/blast/make.py
topiary/external/ncbi/blast/merge.py
topiary/external/ncbi/blast/ncbi.py
topiary/external/ncbi/blast/recip.py
topiary/external/ncbi/blast/util.py
topiary/external/ncbi/entrez/__init__.py
topiary/external/ncbi/entrez/proteome.py
topiary/external/ncbi/entrez/sequences.py
topiary/external/ncbi/entrez/taxid.py
topiary/external/opentree/__init__.py
topiary/external/opentree/ott.py
topiary/external/opentree/tree.py
topiary/external/opentree/util.py
topiary/external/raxml/__init__.py
topiary/external/raxml/_raxml.py
topiary/external/raxml/ancestors.py
topiary/external/raxml/model.py
topiary/external/raxml/tree.py
topiary/io/__init__.py
topiary/io/alignments.py
topiary/io/dataframe.py
topiary/io/seed.py
topiary/io/tree.py
topiary/io/construct/__init__.py
topiary/io/construct/from_seed.py
topiary/io/construct/from_xml.py
topiary/pipeline/__init__.py
topiary/pipeline/alignment_to_ancestors.py
topiary/pipeline/base.py
topiary/pipeline/seed_to_alignment.py
topiary/pipeline/seq_to_alignment.py
topiary/quality/__init__.py
topiary/quality/alignment.py
topiary/quality/taxonomic.py
topiary/quality/redundancy/__init__.py
topiary/quality/redundancy/_block.py
topiary/quality/redundancy/redundancy.py
topiary/util/__init__.py
topiary/util/create_nicknames.py
topiary_asr.egg-info/PKG-INFO
topiary_asr.egg-info/SOURCES.txt
topiary_asr.egg-info/dependency_links.txt
topiary_asr.egg-info/requires.txt
topiary_asr.egg-info/top_level.txt