API Reference Index

Trees

Name	Summary
build_tree	Construct a maximum-likelihood phylogenetic tree.
fit_tree	Fit branch lengths to a phylogenetic tree.
nj_tree	Construct rapid neighbour-joining tree from pairwise distance matrix.
consensus_tree	Construct a consensus tree from a collection of trees.
random_tree	Create a randomly generated phylogenetic tree.

Alignments

Name	Summary
simulate_alignment	Simulate an alignment with AliSim.

Substitution Models

Name	Summary
model_finder	Determine the best-fit model for your data.
ModelFinderResult	Collection of data returned by IQ-TREE's ModelFinder.
Model	Class for substitution models.
make_model	Function to construct Model classes from IQ-TREE strings.
SubstitutionModel	Enums for substitution models.
FreqType	Enum for base frequencies and class for custom base frequencies.
RateModel	Classes for rate heterogeneity.

Genetic Distances

Name	Summary
jc_distances	Pairwise Jukes-Cantor genetic distances.

Tree Distances

Name	Summary
robinson_foulds	Pairwise Robinson-Foulds distances.