LICENSE.txt
README.md
pyproject.toml
setup.py
./configuration.py
./magus.py
./align/__init__.py
./align/aligner.py
./align/alignment_context.py
./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
./tasks/__init__.py
./tasks/controller.py
./tasks/files.py
./tasks/manager.py
./tasks/task.py
./tools/__init__.py
./tools/external_tools.py
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