CONTRIBUTING.md
LICENSE.txt
MANIFEST.in
README.rst
requirements.txt
setup.cfg
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/increment_version.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
prophyle/prophyle_assembler/prophyle_assembler.cpp
prophyle/prophyle_assembler/prophyle_assembler.o
prophyle/prophyle_assignment/Makefile
prophyle/prophyle_assignment/knhx.c
prophyle/prophyle_assignment/knhx.h
prophyle/prophyle_assignment/knhx.o
prophyle/prophyle_assignment/prophyle_assignment
prophyle/prophyle_assignment/prophyle_assignment.cpp
prophyle/prophyle_assignment/prophyle_assignment.o
prophyle/prophyle_assignment/read_processor.cpp
prophyle/prophyle_assignment/read_processor.h
prophyle/prophyle_assignment/read_processor.o
prophyle/prophyle_assignment/tree_index.cpp
prophyle/prophyle_assignment/tree_index.h
prophyle/prophyle_assignment/tree_index.o
prophyle/prophyle_assignment/word_splitter.cpp
prophyle/prophyle_assignment/word_splitter.h
prophyle/prophyle_assignment/word_splitter.o
prophyle/prophyle_index/Makefile
prophyle/prophyle_index/bitarray.c
prophyle/prophyle_index/bitarray.h
prophyle/prophyle_index/bitarray.o
prophyle/prophyle_index/bwa_utils.c
prophyle/prophyle_index/bwa_utils.h
prophyle/prophyle_index/bwa_utils.o
prophyle/prophyle_index/contig_node_translator.c
prophyle/prophyle_index/contig_node_translator.h
prophyle/prophyle_index/contig_node_translator.o
prophyle/prophyle_index/klcp.c
prophyle/prophyle_index/klcp.h
prophyle/prophyle_index/klcp.o
prophyle/prophyle_index/main.c
prophyle/prophyle_index/main.o
prophyle/prophyle_index/prophyle_index
prophyle/prophyle_index/prophyle_index_build.c
prophyle/prophyle_index/prophyle_index_build.h
prophyle/prophyle_index/prophyle_index_build.o
prophyle/prophyle_index/prophyle_query.c
prophyle/prophyle_index/prophyle_query.h
prophyle/prophyle_index/prophyle_query.o
prophyle/prophyle_index/prophyle_utils.c
prophyle/prophyle_index/prophyle_utils.h
prophyle/prophyle_index/prophyle_utils.o
prophyle/prophyle_index/bwa/Makefile
prophyle/prophyle_index/bwa/QSufSort.c
prophyle/prophyle_index/bwa/QSufSort.h
prophyle/prophyle_index/bwa/QSufSort.o
prophyle/prophyle_index/bwa/bamlite.c
prophyle/prophyle_index/bwa/bamlite.h
prophyle/prophyle_index/bwa/bamlite.o
prophyle/prophyle_index/bwa/bntseq.c
prophyle/prophyle_index/bwa/bntseq.h
prophyle/prophyle_index/bwa/bntseq.o
prophyle/prophyle_index/bwa/bwa
prophyle/prophyle_index/bwa/bwa.c
prophyle/prophyle_index/bwa/bwa.h
prophyle/prophyle_index/bwa/bwa.o
prophyle/prophyle_index/bwa/bwamem.c
prophyle/prophyle_index/bwa/bwamem.h
prophyle/prophyle_index/bwa/bwamem.o
prophyle/prophyle_index/bwa/bwamem_extra.c
prophyle/prophyle_index/bwa/bwamem_extra.o
prophyle/prophyle_index/bwa/bwamem_pair.c
prophyle/prophyle_index/bwa/bwamem_pair.o
prophyle/prophyle_index/bwa/bwape.c
prophyle/prophyle_index/bwa/bwape.o
prophyle/prophyle_index/bwa/bwase.c
prophyle/prophyle_index/bwa/bwase.h
prophyle/prophyle_index/bwa/bwase.o
prophyle/prophyle_index/bwa/bwaseqio.c
prophyle/prophyle_index/bwa/bwaseqio.o
prophyle/prophyle_index/bwa/bwashm.c
prophyle/prophyle_index/bwa/bwashm.o
prophyle/prophyle_index/bwa/bwt.c
prophyle/prophyle_index/bwa/bwt.h
prophyle/prophyle_index/bwa/bwt.o
prophyle/prophyle_index/bwa/bwt_gen.c
prophyle/prophyle_index/bwa/bwt_gen.o
prophyle/prophyle_index/bwa/bwt_lite.c
prophyle/prophyle_index/bwa/bwt_lite.h
prophyle/prophyle_index/bwa/bwt_lite.o
prophyle/prophyle_index/bwa/bwtaln.c
prophyle/prophyle_index/bwa/bwtaln.h
prophyle/prophyle_index/bwa/bwtaln.o
prophyle/prophyle_index/bwa/bwtgap.c
prophyle/prophyle_index/bwa/bwtgap.h
prophyle/prophyle_index/bwa/bwtgap.o
prophyle/prophyle_index/bwa/bwtindex.c
prophyle/prophyle_index/bwa/bwtindex.o
prophyle/prophyle_index/bwa/bwtsw2.h
prophyle/prophyle_index/bwa/bwtsw2_aux.c
prophyle/prophyle_index/bwa/bwtsw2_aux.o
prophyle/prophyle_index/bwa/bwtsw2_chain.c
prophyle/prophyle_index/bwa/bwtsw2_chain.o
prophyle/prophyle_index/bwa/bwtsw2_core.c
prophyle/prophyle_index/bwa/bwtsw2_core.o
prophyle/prophyle_index/bwa/bwtsw2_main.c
prophyle/prophyle_index/bwa/bwtsw2_main.o
prophyle/prophyle_index/bwa/bwtsw2_pair.c
prophyle/prophyle_index/bwa/bwtsw2_pair.o
prophyle/prophyle_index/bwa/example.c
prophyle/prophyle_index/bwa/fastmap.c
prophyle/prophyle_index/bwa/fastmap.o
prophyle/prophyle_index/bwa/is.c
prophyle/prophyle_index/bwa/is.o
prophyle/prophyle_index/bwa/kbtree.h
prophyle/prophyle_index/bwa/khash.h
prophyle/prophyle_index/bwa/kopen.c
prophyle/prophyle_index/bwa/kopen.o
prophyle/prophyle_index/bwa/kseq.h
prophyle/prophyle_index/bwa/ksort.h
prophyle/prophyle_index/bwa/kstring.c
prophyle/prophyle_index/bwa/kstring.h
prophyle/prophyle_index/bwa/kstring.o
prophyle/prophyle_index/bwa/ksw.c
prophyle/prophyle_index/bwa/ksw.h
prophyle/prophyle_index/bwa/ksw.o
prophyle/prophyle_index/bwa/kthread.c
prophyle/prophyle_index/bwa/kthread.o
prophyle/prophyle_index/bwa/kvec.h
prophyle/prophyle_index/bwa/main.c
prophyle/prophyle_index/bwa/main.o
prophyle/prophyle_index/bwa/malloc_wrap.c
prophyle/prophyle_index/bwa/malloc_wrap.h
prophyle/prophyle_index/bwa/malloc_wrap.o
prophyle/prophyle_index/bwa/maxk.c
prophyle/prophyle_index/bwa/maxk.o
prophyle/prophyle_index/bwa/pemerge.c
prophyle/prophyle_index/bwa/pemerge.o
prophyle/prophyle_index/bwa/rle.c
prophyle/prophyle_index/bwa/rle.h
prophyle/prophyle_index/bwa/rle.o
prophyle/prophyle_index/bwa/rope.c
prophyle/prophyle_index/bwa/rope.h
prophyle/prophyle_index/bwa/rope.o
prophyle/prophyle_index/bwa/utils.c
prophyle/prophyle_index/bwa/utils.h
prophyle/prophyle_index/bwa/utils.o
prophyle/trees/bacteria.nw
prophyle/trees/hmp.nw
prophyle/trees/plasmids.nw
prophyle/trees/viruses.nw