LICENSE
README.md
pyproject.toml
setup.py
scripts/alignment2iqtree_states.py
scripts/calculate_mutspec.py
scripts/collect_mutations.py
scripts/iqtree_states_add_part.py
scripts/multifasta_coding.py
scripts/select_records.py
src/PyMutSpec.egg-info/PKG-INFO
src/PyMutSpec.egg-info/SOURCES.txt
src/PyMutSpec.egg-info/dependency_links.txt
src/PyMutSpec.egg-info/requires.txt
src/PyMutSpec.egg-info/top_level.txt
src/pymutspec/__init__.py
src/pymutspec/annotation/__init__.py
src/pymutspec/annotation/auxiliary.py
src/pymutspec/annotation/mut.py
src/pymutspec/annotation/spectra.py
src/pymutspec/annotation/tree.py
src/pymutspec/constants/__init__.py
src/pymutspec/constants/sbs.py
src/pymutspec/draw/__init__.py
src/pymutspec/draw/sbs_orders.py
src/pymutspec/draw/spectra.py
src/pymutspec/io/__init__.py
src/pymutspec/io/auxiliary.py
src/pymutspec/io/gb.py
src/pymutspec/io/states.py
src/pymutspec/utils/__init__.py
src/pymutspec/utils/custom_profile.py
src/pymutspec/utils/logging.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