LICENSE.txt
MANIFEST.in
README.rst
setup.cfg
setup.py
docs/Makefile
docs/api.rst
docs/filter.rst
docs/gene.rst
docs/genome.rst
docs/ham.rst
docs/iHam.rst
docs/index.rst
docs/mapper.rst
docs/taxonomy.rst
docs/treeprofile.rst
docs/utils.rst
pyham/TreeProfile.py
pyham/__init__.py
pyham/abstractgene.py
pyham/genome.py
pyham/ham.py
pyham/iham.py
pyham/mapper.py
pyham/parsers.py
pyham/taxonomy.py
pyham/utils.py
pyham.egg-info/PKG-INFO
pyham.egg-info/SOURCES.txt
pyham.egg-info/dependency_links.txt
pyham.egg-info/requires.txt
pyham.egg-info/top_level.txt
tests/functional_test.py
tests/test_abstractgene.py
tests/test_abstractgene.pyc
tests/test_conflict.py
tests/test_conflict.pyc
tests/test_genome.py
tests/test_genome.pyc
tests/test_ham.py
tests/test_ham.pyc
tests/test_iham.py
tests/test_iham.pyc
tests/test_mapper.py
tests/test_mapper.pyc
tests/test_orthoxmlparser.py
tests/test_orthoxmlparser.pyc
tests/test_taxonomy.py
tests/test_taxonomy.pyc
tests/test_treeprofile.py
tests/test_treeprofile.pyc
tests/test_utils.py
tests/test_utils.pyc
tests/data/SimpleEx_complexParalogGetHOGS3format.xml
tests/data/hogvisEx.orthoxml
tests/data/simpleEx.nwk
tests/data/simpleEx.orthoxml
tests/data/simpleEx.phyloxml
tests/data/simpleExNoCladeName.phyloxml
tests/data/simpleExNoName.nwk
tests/data/simpleExNoName.phyloxml
tests/data/simpleEx_complexParalogs.orthoxml