README.md
setup.cfg
setup.py
PHASEfilter/__init__.py
PHASEfilter.egg-info/PKG-INFO
PHASEfilter.egg-info/SOURCES.txt
PHASEfilter.egg-info/dependency_links.txt
PHASEfilter.egg-info/entry_points.txt
PHASEfilter.egg-info/requires.txt
PHASEfilter.egg-info/top_level.txt
PHASEfilter/bin/__init__.py
PHASEfilter/bin/make_alignment.py
PHASEfilter/bin/phasefilter.py
PHASEfilter/bin/phasefilter_single.py
PHASEfilter/bin/reference_statistics.py
PHASEfilter/bin/synchronize_genomes.py
PHASEfilter/lib/__init__.py
PHASEfilter/lib/constants/__init__.py
PHASEfilter/lib/constants/constants.py
PHASEfilter/lib/constants/version.py
PHASEfilter/lib/process/__init__.py
PHASEfilter/lib/process/process_genomes.py
PHASEfilter/lib/process/process_references.py
PHASEfilter/lib/utils/__init__.py
PHASEfilter/lib/utils/blast_two_sequences.py
PHASEfilter/lib/utils/lastz_two_sequences.py
PHASEfilter/lib/utils/lift_over_simple.py
PHASEfilter/lib/utils/read_gff.py
PHASEfilter/lib/utils/reference.py
PHASEfilter/lib/utils/run_extra_software.py
PHASEfilter/lib/utils/software.py
PHASEfilter/lib/utils/testing_software.py
PHASEfilter/lib/utils/util.py
PHASEfilter/lib/utils/vcf_process.py
PHASEfilter/tests/__init__.py
PHASEfilter/tests/test_lift_over.py
PHASEfilter/tests/test_process_genomes.py
PHASEfilter/tests/test_reference.py
PHASEfilter/tests/test_run_extra_software.py
PHASEfilter/tests/test_software.py
PHASEfilter/tests/test_synchronization.py
PHASEfilter/tests/test_utils.py
PHASEfilter/tests/test_vcf.py