LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements.txt
setup.py
PyMutSpec.egg-info/.gitignore
PyMutSpec.egg-info/PKG-INFO
PyMutSpec.egg-info/SOURCES.txt
PyMutSpec.egg-info/dependency_links.txt
PyMutSpec.egg-info/requires.txt
PyMutSpec.egg-info/top_level.txt
pymutspec/__init__.py
pymutspec/annotation/__init__.py
pymutspec/annotation/auxiliary.py
pymutspec/annotation/mut.py
pymutspec/annotation/spectra.py
pymutspec/annotation/tree.py
pymutspec/constants/__init__.py
pymutspec/constants/sbs.py
pymutspec/draw/__init__.py
pymutspec/draw/sbs_orders.py
pymutspec/draw/spectra.py
pymutspec/io/__init__.py
pymutspec/io/auxiliary.py
pymutspec/io/states.py
pymutspec/utils/__init__.py
pymutspec/utils/custom_profile.py
pymutspec/utils/logging.py
pymutspec/utils/configs/log_settings.yaml
scripts/1.terminal_genomes2iqtree_format.py
scripts/2.iqtree_states2custom_format.py
scripts/2.iqtree_states_parted2custom_format.py
scripts/alignment2iqtree_states.py
scripts/calculate_mutspec.py
scripts/collect_mutations.py
scripts/filter_aln.py
scripts/iqtree_states_add_part.py
scripts/multifasta_coding.py
scripts/plot_spectra.py
scripts/qc_aln.py
scripts/raxml_states2iqtree_states.py
scripts/rename_internal_nodes.py
scripts/select_records.py
tests/test_codon_ann.py
tests/test_collect_mutations.py
tests/test_io.py
tests/test_mutspec_calc.py
tests/test_plot_spectrum.py
tests/test_run_main_scripts.py
tests/test_tree_annotation.py