AUTHORS.rst
CONTRIBUTING.rst
HISTORY.rst
LICENSE
MANIFEST.in
README.rst
setup.cfg
setup.py
docs/Makefile
docs/authors.rst
docs/conf.py
docs/contributing.rst
docs/emase.rst
docs/examples.rst
docs/history.rst
docs/index.rst
docs/installation.rst
docs/make.bat
docs/readme.rst
docs/usage.rst
emase/AlignmentMatrixFactory.py
emase/AlignmentPropertyMatrix.py
emase/EMfactory.py
emase/Sparse3DMatrix.py
emase/__init__.py
emase.egg-info/PKG-INFO
emase.egg-info/SOURCES.txt
emase.egg-info/dependency_links.txt
emase.egg-info/not-zip-safe
emase.egg-info/requires.txt
emase.egg-info/top_level.txt
scripts/bam-to-emase
scripts/combine-emase-files
scripts/count-alignments
scripts/count-shared-multireads-pairwise
scripts/prepare-emase
scripts/run-emase
tests/__init__.py
tests/test_emase.py