LICENSE.md
README.md
setup.py
phykit/__init__.py
phykit/__main__.py
phykit/phykit.py
phykit/version.py
phykit.egg-info/PKG-INFO
phykit.egg-info/SOURCES.txt
phykit.egg-info/dependency_links.txt
phykit.egg-info/entry_points.txt
phykit.egg-info/requires.txt
phykit.egg-info/top_level.txt
phykit/helpers/__init__.py
phykit/helpers/boolean_argument_parsing.py
phykit/helpers/files.py
phykit/helpers/stats_summary.py
phykit/services/__init__.py
phykit/services/base.py
phykit/services/alignment/__init__.py
phykit/services/alignment/alignment_length.py
phykit/services/alignment/alignment_length_no_gaps.py
phykit/services/alignment/base.py
phykit/services/alignment/column_score.py
phykit/services/alignment/create_concatenation_matrix.py
phykit/services/alignment/dna_threader.py
phykit/services/alignment/faidx.py
phykit/services/alignment/gc_content.py
phykit/services/alignment/pairwise_identity.py
phykit/services/alignment/parsimony_informative_sites.py
phykit/services/alignment/rcv.py
phykit/services/alignment/rename_fasta_entries.py
phykit/services/alignment/sum_of_pairs_score.py
phykit/services/alignment/variable_sites.py
phykit/services/tree/__init__.py
phykit/services/tree/base.py
phykit/services/tree/bipartition_support_stats.py
phykit/services/tree/branch_length_multiplier.py
phykit/services/tree/collapse_branches.py
phykit/services/tree/covarying_evolutionary_rates.py
phykit/services/tree/dvmc.py
phykit/services/tree/evolutionary_rate.py
phykit/services/tree/internal_branch_stats.py
phykit/services/tree/internode_labeler.py
phykit/services/tree/last_common_ancestor_subtree.py
phykit/services/tree/lb_score.py
phykit/services/tree/patristic_distances.py
phykit/services/tree/polytomy_test.py
phykit/services/tree/print_tree.py
phykit/services/tree/prune_tree.py
phykit/services/tree/rename_tree_tips.py
phykit/services/tree/rf_distance.py
phykit/services/tree/saturation.py
phykit/services/tree/spurious_sequence.py
phykit/services/tree/tip_labels.py
phykit/services/tree/total_tree_length.py
phykit/services/tree/treeness.py
phykit/services/tree/treeness_over_rcv.py