Neighbor joining
Neighbor joining is similar to UPGMA/WPGMA, but infers unrooted trees. As a consequence, and unlike UPGMA/WPGMA, it does not require that the multiple sequen...
Recent posts
UPGMA and WPGMA trees
Two related methods for infer phylogenetic trees from multiple sequence alignments (MSAs) are the Unweighted Pair Group Method with Arithmetic Mean (UPMGA) a...
GTR and nested models
The most commonly used nucleotide substitution models for phylogenetic reconstruction belong to the general time reversible (GTR) family. The main reason for...
Tree comparisons
The crudest way to compare two trees is to somehow quantify the difference between them as a single number. There are many methods of quantifying the differe...
Phylogenetic trees and data structures
Bifurcating trees have found enormous utility in biology. Depending on what the tips of a tree represent, they can be used as a model to help understand vari...