Bootstrap Test of Phylogeny

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 A tree reconstructed from the observed sequence or other appropriate data using any tree-making method (such as UPGMA, NJ, ME, or MP) is known as an inferred or reconstructed tree.RH_Inferred_tree is Felsenstein's (1985)Felsenstein_1985 bootstrap test, which is evaluated using Efron's (1982)Efron_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 The branching pattern of a tree is its topology.RH_Topology of this tree is compared to that of the original tree.  Each interior branch A branch is a line connecting either two internal nodes to each other or an external node to an internal node in a phylogenetic tree. The length of a branch denotes the genetic distance (e.g., number of substitutions per unit time) between the two taxa it connects. 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 A branch is a line connecting either two internal nodes to each other or an external node to an internal node in a phylogenetic tree. The length of a branch denotes the genetic distance (e.g., number of substitutions per unit time) between the two taxa it connects. 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 A branch is a line connecting either two internal nodes to each other or an external node to an internal node in a phylogenetic tree. The length of a branch denotes the genetic distance (e.g., number of substitutions per unit time) between the two taxa it connects. is 95% or higher, then the topology The branching pattern of a tree is its topology. at that branch A branch is a line connecting either two internal nodes to each other or an external node to an internal node in a phylogenetic tree. The length of a branch denotes the genetic distance (e.g., number of substitutions per unit time) between the two taxa it connects. is considered "correct".  See Nei and Kumar (2000)Nei_and_Kumar_2000 (chapter 9) for further details.

This test is available for four different methods: Neighbor JoiningHC_Neighbor_Joining, Minimum EvolutionHC_Minimum_Evolution, Maximum ParsimonyHC_Maximum_Parsimony, UPGMAHC_UPGMA, and Maximum Likelihood.