CONTRIBUTING.md
LICENSE.txt
MANIFEST.in
README.rst
requirements.txt
setup.py
prophyle/1step_match.py
prophyle/Makefile
prophyle/__init__.py
prophyle/_all_kmers.py
prophyle/_fa_norm.py
prophyle/_fa_to_kmers.py
prophyle/prophyle.py
prophyle/prophyle_analyze.py
prophyle/prophyle_assignment.py
prophyle/prophyle_ncbi_tree.py
prophyle/prophyle_oldrefseq.py
prophyle/prophyle_otu_table.py
prophyle/prophyle_paired_end.py
prophyle/prophyle_parse_rpt.py
prophyle/prophyle_plot_tree.py
prophyle/prophyle_propagation_makefile.py
prophyle/prophyle_propagation_postprocessing.py
prophyle/prophyle_propagation_preprocessing.py
prophyle/prophyle_split_allseq.py
prophyle/prophyle_validate_tree.py
prophyle/prophylelib.py
prophyle/tree_print_fasta_names.py
prophyle/version.py
prophyle.egg-info/PKG-INFO
prophyle.egg-info/SOURCES.txt
prophyle.egg-info/dependency_links.txt
prophyle.egg-info/entry_points.txt
prophyle.egg-info/requires.txt
prophyle.egg-info/top_level.txt
prophyle/prophyle_assembler/Makefile
prophyle/prophyle_assembler/kseq.h
prophyle/prophyle_assembler/prophyle_assembler.cpp
prophyle/prophyle_assignment/Makefile
prophyle/prophyle_assignment/knhx.c
prophyle/prophyle_assignment/knhx.h
prophyle/prophyle_assignment/prophyle_assignment.cpp
prophyle/prophyle_assignment/read_processor.cpp
prophyle/prophyle_assignment/read_processor.h
prophyle/prophyle_assignment/tree_index.cpp
prophyle/prophyle_assignment/tree_index.h
prophyle/prophyle_assignment/word_splitter.cpp
prophyle/prophyle_assignment/word_splitter.h
prophyle/prophyle_index/Makefile
prophyle/prophyle_index/bitarray.c
prophyle/prophyle_index/bitarray.h
prophyle/prophyle_index/bwa_utils.c
prophyle/prophyle_index/bwa_utils.h
prophyle/prophyle_index/contig_node_translator.c
prophyle/prophyle_index/contig_node_translator.h
prophyle/prophyle_index/klcp.c
prophyle/prophyle_index/klcp.h
prophyle/prophyle_index/main.c
prophyle/prophyle_index/prophyle_index_build.c
prophyle/prophyle_index/prophyle_index_build.h
prophyle/prophyle_index/prophyle_query.c
prophyle/prophyle_index/prophyle_query.h
prophyle/prophyle_index/prophyle_utils.c
prophyle/prophyle_index/prophyle_utils.h
prophyle/trees/bacteria.nw
prophyle/trees/hmp.nw
prophyle/trees/plasmids.nw
prophyle/trees/viruses.nw