Resolution and support for branches differed based on the combination of markers used for each genus.
The bootstrap support for branches in maximum parsimony, distance and maximum likelihood estimation, or posterior probabilities in Bayesian inference, measure the uncertainty about a branch due to the sampling of the sites from genes or sampling genes from genomes.
The degree of statistical support for branches was determined with 1000 bootstrap replicates.
Our approach included performing bootstrap and Bremer decay index analyses to measure support for branches.
For DNA and amino acid analyses, support for branches was assessed by bootstrap analyses of 500 replicates.
Statistical support for branching order was estimated from 100 bootstrap replications generated using SEQBOOT, using the CONSENSUS programme.
The optimum ML tree was inferred in RaxML with branch lengths optimized in PAUP* is shown in Figure 3. Topological support for branches was assessed from the consensus of 1,000 ML bootstrap trees inferred in RAxML and GARLI.
Phylogenetic relationships amongst individual housekeeping alleles was examined using the neighbor joining (NJ) method with Jukes-Cantor substitution algorithm model as implemented in MEGA4 [43]; bootstrapping (1000 replicates) was used to ascertain support for branches.
Similarly, bootstrap and jackknife measures of topological stability (nodal reliability) are also inversely correlated with number of taxa, and their usefulness in assessing support for branches is therefore artifactually limited in large-scale (>100 taxa) phylogeny reconstructions [37].
The two algorithms are quite different however, in detail, and mBed does have some features, for example support for branch-lengths, which make the method interesting as an alternative.
Support for branches was estimated with bootstrap analysis (n = 1000).
