README.md
setup.py
sisrs/__init__.py
sisrs/align_contigs.py
sisrs/change_missing.py
sisrs/command.py
sisrs/filter_nexus_for_missing.py
sisrs/get_alignment.py
sisrs/get_pruned_dict.py
sisrs/identify_fixed_sites.py
sisrs/output_alignment.py
sisrs/process.py
sisrs/sisrs.py
sisrs/specific_genome.py
sisrs/sub_sample_for_velvet_unshuff.py
sisrs/subsample.py
sisrs.egg-info/PKG-INFO
sisrs.egg-info/SOURCES.txt
sisrs.egg-info/dependency_links.txt
sisrs.egg-info/entry_points.txt
sisrs.egg-info/requires.txt
sisrs.egg-info/top_level.txt
sisrs/aligners/__init__.py
sisrs/aligners/aligner.py
sisrs/aligners/bowtie2.py