What is a bootstrap value?
In the context of phylogenetics, bootstrap proportions are a measure of support from within a data set for a particular node. Bootstrap proportions are obtained by resampling individual sites from an alignment, with replacement, generating number of replicate alignments. For each of these alignment replicates, the best tree is estimated. The bootstrap proportion for a node is the number of times (usually measured as a percent) that that particular node is recovered in all of the replicates.
