CHANGELOG
CONTRIBUTORS.txt
LICENSE.txt
MANIFEST.in
README.rst
setup.cfg
setup.py
data/indelible/control.1.txt
data/indelible/control.2.txt
data/indelible/control.3.txt
data/indelible/control.4.txt
data/indelible/control.supp.test1.txt
data/indelible/control.supp.test2.txt
data/reference_alleles/my_reference_allele_file.test2.txt
data/reference_alleles/my_reference_allele_file.txt
data/settings/ngsphy.settings.1.txt
data/settings/ngsphy.settings.2.txt
data/settings/ngsphy.settings.3.txt
data/settings/ngsphy.settings.4.txt
data/settings/ngsphy.settings.supp.test1.txt
data/settings/ngsphy.settings.supp.test2.100x.txt
data/settings/ngsphy.settings.supp.test2.10x.txt
data/settings/ngsphy.settings.supp.test2.200x.rc.txt
data/settings/ngsphy.settings.supp.test2.200x.txt
data/settings/ngsphy.settings.supp.test2.20x.txt
data/settings/ngsphy.settings.supp.test2.2x.txt
data/trees/supp.test1.tree
data/trees/supp.test2.tree
data/trees/t1.tree
data/trees/t2.tree
data/trees/t3.tree
ngsphy/__init__.py
ngsphy/__main__.py
ngsphy/coverage.py
ngsphy/individual.py
ngsphy/loggingformatter.py
ngsphy/msatools.py
ngsphy/ngsphy.py
ngsphy/ngsphyexceptions.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