Phylogeny | Construct/Test Neighbor-Joining Tree

Or

Phylogeny | Construct/Test Minimum-Evolution Tree

Or

Phylogeny | Construct/Test UPGMA Tree

Or

Phylogeny | Construct/Test Maximum Likelihood Tree

Or

Phylogeny | Construct/Test Maximum Parsimony Tree(s)

One of the most commonly used tests of the reliability of an inferred tree is Felsenstein's (1985) bootstrap test, which is evaluated using Efron's (1982) bootstrap resampling technique. If there are m sequences, each with n nucleotides (or codons or amino acids), a phylogenetic tree can be reconstructed using some tree building method. From each sequence, n nucleotides are randomly chosen with replacements, giving rise to m rows of n columns each. These now constitute a new set of sequences. A tree is then reconstructed with these new sequences using the same tree building method as before. Next the topology of this tree is compared to that of the original tree. Each interior branch of the original tree that is different from the bootstrap tree the sequence it partitions is given a score of 0; all other interior branches are given the value 1. This procedure of resampling the sites and the subsequent tree reconstruction is repeated several hundred times, and the percentage of times each interior branch is given a value of 1 is noted. This is known as the bootstrap value. As a general rule, if the bootstrap value for a given interior branch is 95% or higher, then the topology at that branch is considered "correct". See Nei and Kumar (2000) (chapter 9) for further details.

This test is available for four different methods: Neighbor Joining, Minimum Evolution, Maximum Parsimony, UPGMA, and Maximum Likelihood.