Software creates large samples of phylogenetic trees. How often a particular group of sequences occurs in the sample can indicate the amount of support for that group. The bootstrapping approach (A) involves generating pseudo-replicate data sets by re-sampling – with replacement – the sites in the original data matrix. Trees are produced from each of the pseudo-replicate data sets by performing tree searches or using a tree-building algorithm. The proportion of trees that contains a group is often interpreted as an assessment of repeatability – the probability that the grouping would be recovered with another data set. The Markov chain Monte Carlo methodology (B) does not alter the data. Instead a chain of trees is produced by starting from an initial tree, proposing random perturbations, and either accepting or rejecting these proposals according to specific rules (which take into account the likelihood of the proposed tree). MCMC is usually used ...
New Growth in Phylogeny Programs
Sometimes, the number of times a paper has been cited barely begins to describe the importance of the work.
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