README.rst
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/contig_statistics.py
prophyle/prophyle.py
prophyle/prophyle_assignment.py
prophyle/prophyle_merge_fa.py
prophyle/prophyle_merge_trees.py
prophyle/prophyle_ncbi_tree.py
prophyle/prophyle_propagation_makefile.py
prophyle/prophyle_test_tree.py
prophyle/split_allseq.py
prophyle/tree_annotate_kmers.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_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/prophyle_index/bwa/Makefile
prophyle/prophyle_index/bwa/QSufSort.c
prophyle/prophyle_index/bwa/QSufSort.h
prophyle/prophyle_index/bwa/bamlite.c
prophyle/prophyle_index/bwa/bamlite.h
prophyle/prophyle_index/bwa/bntseq.c
prophyle/prophyle_index/bwa/bntseq.h
prophyle/prophyle_index/bwa/bwa.c
prophyle/prophyle_index/bwa/bwa.h
prophyle/prophyle_index/bwa/bwamem.c
prophyle/prophyle_index/bwa/bwamem.h
prophyle/prophyle_index/bwa/bwamem_extra.c
prophyle/prophyle_index/bwa/bwamem_pair.c
prophyle/prophyle_index/bwa/bwape.c
prophyle/prophyle_index/bwa/bwase.c
prophyle/prophyle_index/bwa/bwase.h
prophyle/prophyle_index/bwa/bwaseqio.c
prophyle/prophyle_index/bwa/bwashm.c
prophyle/prophyle_index/bwa/bwt.c
prophyle/prophyle_index/bwa/bwt.h
prophyle/prophyle_index/bwa/bwt_gen.c
prophyle/prophyle_index/bwa/bwt_lite.c
prophyle/prophyle_index/bwa/bwt_lite.h
prophyle/prophyle_index/bwa/bwtaln.c
prophyle/prophyle_index/bwa/bwtaln.h
prophyle/prophyle_index/bwa/bwtgap.c
prophyle/prophyle_index/bwa/bwtgap.h
prophyle/prophyle_index/bwa/bwtindex.c
prophyle/prophyle_index/bwa/bwtsw2.h
prophyle/prophyle_index/bwa/bwtsw2_aux.c
prophyle/prophyle_index/bwa/bwtsw2_chain.c
prophyle/prophyle_index/bwa/bwtsw2_core.c
prophyle/prophyle_index/bwa/bwtsw2_main.c
prophyle/prophyle_index/bwa/bwtsw2_pair.c
prophyle/prophyle_index/bwa/example.c
prophyle/prophyle_index/bwa/fastmap.c
prophyle/prophyle_index/bwa/is.c
prophyle/prophyle_index/bwa/kbtree.h
prophyle/prophyle_index/bwa/khash.h
prophyle/prophyle_index/bwa/kopen.c
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/ksw.c
prophyle/prophyle_index/bwa/ksw.h
prophyle/prophyle_index/bwa/kthread.c
prophyle/prophyle_index/bwa/kvec.h
prophyle/prophyle_index/bwa/main.c
prophyle/prophyle_index/bwa/malloc_wrap.c
prophyle/prophyle_index/bwa/malloc_wrap.h
prophyle/prophyle_index/bwa/maxk.c
prophyle/prophyle_index/bwa/pemerge.c
prophyle/prophyle_index/bwa/rle.c
prophyle/prophyle_index/bwa/rle.h
prophyle/prophyle_index/bwa/rope.c
prophyle/prophyle_index/bwa/rope.h
prophyle/prophyle_index/bwa/utils.c
prophyle/prophyle_index/bwa/utils.h
prophyle/trees/all.nw
prophyle/trees/bacteria.nw
prophyle/trees/hmp.nw
prophyle/trees/plasmids.nw
prophyle/trees/test_all.nw
prophyle/trees/test_bacteria.nw
prophyle/trees/test_hmp.nw
prophyle/trees/test_plasmids.nw
prophyle/trees/test_viruses.nw
prophyle/trees/viruses.nw