Building phylogenies

Building A Phylogenetic Tree From Pairwise Distances

Directly via alignment.quick_tree()

Directly via alignment.quick_tree() with a third-party hook

You can use the IQ-TREE rapid-NJ algorithm for quick_tree() by installing piqtree and setting use_hook="piqtree".

Using the DistanceMatrix object

Explicitly via DistanceMatrix and cogent3.phylo.nj.nj()`

Directly from a pairwise distance dict

By Least-squares

We illustrate the phylogeny reconstruction by least-squares using the F81 substitution model. We use the advanced-stepwise addition algorithm to search tree space. Here a is the number of taxa to exhaustively evaluate all possible phylogenies for. Successive taxa are added to the top k trees (measured by the least-squares metric) and k trees are kept at each iteration.

Other optional arguments that can be passed to the trex method are: return_all, whether the k best trees at the final step are returned as a ScoredTreeCollection object; order, a series of tip names whose order defines the sequence in which tips will be added during tree building (this allows the user to randomise the input order).

By ML

We illustrate the phylogeny reconstruction using maximum-likelihood using the F81 substitution model. We use the advanced-stepwise addition algorithm to search tree space.