CHANGELOG
CONTRIBUTORS.txt
LICENSE.txt
MANIFEST.in
README.rst
setup.cfg
setup.py
data/test_wrapper.zip
data/indelible/control.1.txt
data/indelible/control.2.txt
data/indelible/control.3.txt
data/indelible/control.4.txt
data/indelible/control.txt
data/settings/settings.10.txt
data/settings/settings.2.txt
data/settings/settings.3.txt
data/settings/settings.4.txt
data/settings/settings.cov.txt
data/settings/settings.indelible.txt
data/settings/settings.ngsphy.1.txt
data/settings/settings.ngsphy.2.txt
data/settings/settings.ngsphy.3.txt
data/settings/settings.ngsphy.4.txt
data/settings/settings.ngsphy.5.txt
data/settings/settings.ngsphy.6.txt
data/settings/settings.readcounts.0.txt
data/settings/settings.readcounts.1.txt
data/settings/settings.readcounts.txt
data/settings/settings.txt
data/trees/t1.tree
data/trees/t2.tree
data/trees/t3.tree
data/trees/t4.tree
data/trees/t5.tree
data/trees/t6.tree
ngsphy/__init__.py
ngsphy/__main__.py
ngsphy/coverage.py
ngsphy/individual.py
ngsphy/loggingformatter.py
ngsphy/msatools.py
ngsphy/ngsphy.py
ngsphy/readcounts.py
ngsphy/reads.py
ngsphy/rerooter.py
ngsphy/sequence.py
ngsphy/settings.py
ngsphy.egg-info/PKG-INFO
ngsphy.egg-info/SOURCES.txt
ngsphy.egg-info/dependency_links.txt
ngsphy.egg-info/entry_points.txt
ngsphy.egg-info/not-zip-safe
ngsphy.egg-info/requires.txt
ngsphy.egg-info/top_level.txt
scripts/ngsphy