piqtree
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GitHub
piqtree
GitHub
Introduction
Quickstart
Quickstart
Construct a maximum likelihood phylogenetic tree
Fit branch lengths to a tree topology from an alignment
Simulate alignments with AliSim
Use different kinds of substitution models
Find the model of best fit with ModelFinder
Calculate pairwise Jukes-Cantor distances
Construct a rapid neighbour-joining tree from a distance matrix
Construct a consensus tree from a collection of trees
Make a randomly generated phylogenetic tree
Calculate pairwise Robinson-Foulds distances between trees
Available substitution models
Available state frequency options
Available rate-heterogeneity options
Apps
Apps
The available piqtree apps
Selecting models for phylogenetic analysis
Estimate a phylogenetic tree
Fit a model to one tree
Pairwise JC distances
NJ tree
Parallel processing across alignments
API reference
API reference
Trees
Trees
build_tree
fit_tree
nj_tree
consensus_tree
random_tree
Alignments
Alignments
simulate_alignment
Substitution models
Substitution models
model_finder
ModelFinderResult
Model
make_model
SubstitutionModel
FreqType
RateModel
Genetic distances
Genetic distances
jc_distances
Tree distances
Tree distances
robinson_foulds
Contributing
Contributing
Setting up your environment for development
Working with the IQ-TREE submodule
Contributing to piqtree
Testing, linting, and type checking
Troubleshooting
Release checklist
Citation
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