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