LICENSE.md
README.md
setup.py
orthohmm/__init__.py
orthohmm/__main__.py
orthohmm/args_processing.py
orthohmm/externals.py
orthohmm/files.py
orthohmm/helpers.py
orthohmm/orthohmm.py
orthohmm/parser.py
orthohmm/version.py
orthohmm/writer.py
orthohmm.egg-info/PKG-INFO
orthohmm.egg-info/SOURCES.txt
orthohmm.egg-info/dependency_links.txt
orthohmm.egg-info/entry_points.txt
orthohmm.egg-info/requires.txt
orthohmm.egg-info/top_level.txt
orthohmm/search/__init__.py
orthohmm/search/engine.py
orthohmm/search/evalue.py
orthohmm/search/matrices.py
orthohmm/search/msa_center_star.py
orthohmm/search/msa_profile.py
orthohmm/search/prefilter.py
orthohmm/search/profile.py
orthohmm/search/sequences.py
orthohmm/search/species_prune.py
orthohmm/search/viterbi.py
orthohmm/search/viterbi_cuda_ctypes.py
orthohmm/search/csrc/hmm_viterbi.c
orthohmm/search/csrc/hmm_viterbi.so
orthohmm/search/csrc/hmm_viterbi_cuda.cu
orthohmm/search/csrc/hmm_viterbi_cuda.so
orthohmm/search/csrc/kmer_prefilter.c
orthohmm/search/csrc/kmer_prefilter.so
orthohmm/search/csrc/pair_align.c
orthohmm/search/csrc/pair_align.so