LICENSE.md
MANIFEST.in
README.rst
setup.cfg
setup.py
sonicparanoid/__init__.py
sonicparanoid/blast_tools.py
sonicparanoid/colored_output.py
sonicparanoid/compile_inpyranoid_c.py
sonicparanoid/compile_mmseqs_parser_c.py
sonicparanoid/extract_results.py
sonicparanoid/get_mmseqs2.py
sonicparanoid/get_test_data.py
sonicparanoid/inpyranoid.py
sonicparanoid/inpyranoid_c.pyx
sonicparanoid/length_difference_filter.py
sonicparanoid/mmseqs_parser_c.pyx
sonicparanoid/mmseqs_parser_cython.py
sonicparanoid/ortholog_detection.py
sonicparanoid/process_output.py
sonicparanoid/reads_stats.py
sonicparanoid/seq_tools.py
sonicparanoid/set_mmseqs2.py
sonicparanoid/setup_sonicparanoid.py
sonicparanoid/sonic_paranoid.py
sonicparanoid/sonic_paranoid_extract.py
sonicparanoid/sys_tools.py
sonicparanoid/test_blast_tools.py
sonicparanoid/test_length_difference_filter.py
sonicparanoid/test_mmseqs_parser_cython.py
sonicparanoid/test_ortholog_detection.py
sonicparanoid/test_reads_stats.py
sonicparanoid/test_seq_tools.py
sonicparanoid/test_sonicparanoid.py
sonicparanoid/test_sys_tools.py
sonicparanoid/test_workers.py
sonicparanoid/workers.py
sonicparanoid.egg-info/PKG-INFO
sonicparanoid.egg-info/SOURCES.txt
sonicparanoid.egg-info/dependency_links.txt
sonicparanoid.egg-info/entry_points.txt
sonicparanoid.egg-info/not-zip-safe
sonicparanoid.egg-info/requires.txt
sonicparanoid.egg-info/top_level.txt
sonicparanoid/bin/README.txt
sonicparanoid/example/test_input/chlamydia_trachomatis
sonicparanoid/example/test_input/deinococcus_radiodurans
sonicparanoid/example/test_input/gloeobacter_violaceus
sonicparanoid/example/test_input/thermotoga_maritima
sonicparanoid/example/test_output/README.txt
sonicparanoid/mmseqs2_src/README.txt
sonicparanoid/mmseqs2_src/mmseqs.tar.gz
sonicparanoid/quick_multi_paranoid/Makefile
sonicparanoid/quick_multi_paranoid/Makefile.in
sonicparanoid/quick_multi_paranoid/config
sonicparanoid/quick_multi_paranoid/dump.cpp
sonicparanoid/quick_multi_paranoid/gen_header.cpp
sonicparanoid/quick_multi_paranoid/hashtable.c
sonicparanoid/quick_multi_paranoid/hashtable.h
sonicparanoid/quick_multi_paranoid/hashtable.o
sonicparanoid/quick_multi_paranoid/hashtable_itr.c
sonicparanoid/quick_multi_paranoid/hashtable_itr.h
sonicparanoid/quick_multi_paranoid/hashtable_private.h
sonicparanoid/quick_multi_paranoid/ortholog.c
sonicparanoid/quick_multi_paranoid/qa.h
sonicparanoid/quick_multi_paranoid/qa1
sonicparanoid/quick_multi_paranoid/qa1.cpp
sonicparanoid/quick_multi_paranoid/qa2
sonicparanoid/quick_multi_paranoid/qa2.cpp
sonicparanoid/quick_multi_paranoid/qp
sonicparanoid/quick_multi_paranoid/qp.c
sonicparanoid/quick_multi_paranoid/qps.c