Quickstart

Want to jump right in to using piqtree? This is the place to be! Here, you can find examples to:

• 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.
• Display substitution models.
• Display frequency options.
• Display rate-heterogeneity options.
• Using the piqtree cogent3 apps.

Be sure to check out the API Reference for full usage!