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