MANIFEST.in
README.md
setup.py
bin/bootstrap
bin/collapse
bin/npbs.py
bin/pre_npbs.py
bin/seqconvert
bin/simulator
bin/treeCl
extensions/tree_collection/cython/py_wrapper.pyx
extensions/tree_collection/cython/wrapper.cpp
extensions/tree_collection/cython/wrapper.pxd
extensions/tree_collection/src/MinSqTree.cc
extensions/tree_collection/src/MinSqTree.h
extensions/tree_collection/src/PhyTree.h
extensions/tree_collection/src/ProblemParser.cc
extensions/tree_collection/src/ProblemParser.h
extensions/tree_collection/src/newick.cc
extensions/tree_collection/src/newick.h
tests/__init__.py
tests/test.py
treeCl/__init__.py
treeCl/alignment.py
treeCl/clustering.py
treeCl/collection.py
treeCl/concatenation.py
treeCl/constants.py
treeCl/distance_matrix.py
treeCl/errors.py
treeCl/parameters.py
treeCl/parsers.py
treeCl/partition.py
treeCl/parutils.py
treeCl/plotter.py
treeCl/simulator.py
treeCl/tasks.py
treeCl/tree.py
treeCl/treedist.py
treeCl.egg-info/PKG-INFO
treeCl.egg-info/SOURCES.txt
treeCl.egg-info/dependency_links.txt
treeCl.egg-info/requires.txt
treeCl.egg-info/top_level.txt
treeCl/logging/logging.yaml
treeCl/utils/__init__.py
treeCl/utils/ambiguate.py
treeCl/utils/decorators.py
treeCl/utils/enum.py
treeCl/utils/fileIO.py
treeCl/utils/gapmasker.py
treeCl/utils/kelley.py
treeCl/utils/kendallcolijn.py
treeCl/utils/math.py
treeCl/utils/misc.py
treeCl/utils/printing.py
treeCl/utils/silhouette.py
treeCl/utils/translator.py
treeCl/wrappers/__init__.py
treeCl/wrappers/abstract_wrapper.py
treeCl/wrappers/aligners.py
treeCl/wrappers/phylogenetics.py