CHANGELOG
LICENSE
MANIFEST.in
README.rst
pyproject.toml
requirements.txt
setup.py
witch.py
bin/witch-msa
tests/__init__.py
tests/test_pipeline.py
witch_msa/__init__.py
witch_msa/configs.py
witch_msa/default.config
witch_msa/init_configs.py
witch_msa.egg-info/PKG-INFO
witch_msa.egg-info/SOURCES.txt
witch_msa.egg-info/dependency_links.txt
witch_msa.egg-info/requires.txt
witch_msa.egg-info/top_level.txt
witch_msa/gcmm/__init__.py
witch_msa/gcmm/algorithm.py
witch_msa/gcmm/aligner.py
witch_msa/gcmm/backbone.py
witch_msa/gcmm/callback.py
witch_msa/gcmm/decompose_tree.py
witch_msa/gcmm/gcmm.py
witch_msa/gcmm/loader.py
witch_msa/gcmm/merger.py
witch_msa/gcmm/results_handler.py
witch_msa/gcmm/task.py
witch_msa/gcmm/tree.py
witch_msa/gcmm/weighting.py
witch_msa/helpers/__init__.py
witch_msa/helpers/alignment_tools.py
witch_msa/helpers/general_tools.py
witch_msa/helpers/math_utils.py
witch_msa/helpers/pyhmmer_tools.py
witch_msa/tools/macOS/FastTreeMP
witch_msa/tools/macOS/hmmalign
witch_msa/tools/macOS/hmmbuild
witch_msa/tools/macOS/hmmsearch
witch_msa/tools/macOS/mafft
witch_msa/tools/macOS/mcl
witch_msa/tools/magus/README.md
witch_msa/tools/magus/configuration.py
witch_msa/tools/magus/magus.py
witch_msa/tools/magus/align/__init__.py
witch_msa/tools/magus/align/aligner.py
witch_msa/tools/magus/align/alignment_context.py
witch_msa/tools/magus/align/decompose/__init__.py
witch_msa/tools/magus/align/decompose/decomposer.py
witch_msa/tools/magus/align/decompose/initial_tree.py
witch_msa/tools/magus/align/decompose/kmh.py
witch_msa/tools/magus/align/merge/__init__.py
witch_msa/tools/magus/align/merge/alignment_graph.py
witch_msa/tools/magus/align/merge/alignment_writer.py
witch_msa/tools/magus/align/merge/merger.py
witch_msa/tools/magus/align/merge/optimizer.py
witch_msa/tools/magus/align/merge/graph_build/__init__.py
witch_msa/tools/magus/align/merge/graph_build/graph_builder.py
witch_msa/tools/magus/align/merge/graph_cluster/__init__.py
witch_msa/tools/magus/align/merge/graph_cluster/clean_clusters.py
witch_msa/tools/magus/align/merge/graph_cluster/clusterer.py
witch_msa/tools/magus/align/merge/graph_cluster/mcl.py
witch_msa/tools/magus/align/merge/graph_cluster/mlr_mcl.py
witch_msa/tools/magus/align/merge/graph_cluster/rg.py
witch_msa/tools/magus/align/merge/graph_trace/__init__.py
witch_msa/tools/magus/align/merge/graph_trace/fm.py
witch_msa/tools/magus/align/merge/graph_trace/min_clusters.py
witch_msa/tools/magus/align/merge/graph_trace/mwt_search.py
witch_msa/tools/magus/align/merge/graph_trace/naive.py
witch_msa/tools/magus/align/merge/graph_trace/rg_fast_search.py
witch_msa/tools/magus/align/merge/graph_trace/rg_search.py
witch_msa/tools/magus/align/merge/graph_trace/tracer.py
witch_msa/tools/magus/helpers/__init__.py
witch_msa/tools/magus/helpers/hmmutils.py
witch_msa/tools/magus/helpers/sequenceutils.py
witch_msa/tools/magus/helpers/treeutils.py
witch_msa/tools/magus/tasks/__init__.py
witch_msa/tools/magus/tasks/controller.py
witch_msa/tools/magus/tasks/files.py
witch_msa/tools/magus/tasks/manager.py
witch_msa/tools/magus/tasks/task.py
witch_msa/tools/magus/tools/__init__.py
witch_msa/tools/magus/tools/external_tools.py
witch_msa/tools/magus/tools/clustal/clustalo
witch_msa/tools/magus/tools/fasttree/FastTree
witch_msa/tools/magus/tools/fasttree/FastTreeMP
witch_msa/tools/magus/tools/hmmer/hmmalign
witch_msa/tools/magus/tools/hmmer/hmmbuild
witch_msa/tools/magus/tools/hmmer/hmmsearch
witch_msa/tools/magus/tools/mafft/mafft
witch_msa/tools/magus/tools/mafft/mafftdir/bin/mafft
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/addsingle
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/contrafoldwrap
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/countlen
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dash_client
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/disttbfast
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndblast
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndfast7
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndpre
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dvtditr
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/f2cl
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/getlag
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/hex2maffttext
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-distance
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-homologs.1
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-profile
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft.1
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafftash_premafft.pl
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/maffttext2hex
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/makedirectionlist
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mccaskillwrap
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/multi2hat3s
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/nodepair
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairash
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairlocalalign
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/regtable2seq
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/replaceu
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/restoreu
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/score
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seekquencer_premafft.pl
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seq2regtable
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setcore
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setdirection
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/sextet5
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/splittbfast
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/tbfast
witch_msa/tools/magus/tools/mafft/mafftdir/libexec/version
witch_msa/tools/magus/tools/mcl/bin/clm
witch_msa/tools/magus/tools/mcl/bin/clmformat
witch_msa/tools/magus/tools/mcl/bin/clxdo
witch_msa/tools/magus/tools/mcl/bin/mcl
witch_msa/tools/magus/tools/mcl/bin/mclblastline
witch_msa/tools/magus/tools/mcl/bin/mclcm
witch_msa/tools/magus/tools/mcl/bin/mclpipeline
witch_msa/tools/magus/tools/mcl/bin/mcx
witch_msa/tools/magus/tools/mcl/bin/mcxarray
witch_msa/tools/magus/tools/mcl/bin/mcxassemble
witch_msa/tools/magus/tools/mcl/bin/mcxdeblast
witch_msa/tools/magus/tools/mcl/bin/mcxdump
witch_msa/tools/magus/tools/mcl/bin/mcxi
witch_msa/tools/magus/tools/mcl/bin/mcxload
witch_msa/tools/magus/tools/mcl/bin/mcxmap
witch_msa/tools/magus/tools/mcl/bin/mcxrand
witch_msa/tools/magus/tools/mcl/bin/mcxsubs
witch_msa/tools/magus/tools/mlrmcl/README
witch_msa/tools/magus/tools/mlrmcl/mlrmcl
witch_msa/tools/magus/tools/mlrmcl/ncut
witch_msa/tools/magus/tools/raxmlng/raxml-ng