Tree files from parsimony, maximum likelihood, and Bayesian analyses were used to draw trees in PAUP*.
Based on our algorithms, a web-based system using input tree files from TreeBASE is also implemented.
Nexus formatted tree files were edited in TreeView [68].
Tree files from both Bayesian and parsimony analyses were used to draw trees in PAUP*.
Tree files were analyzed, viewed and prepared for publication using Dendroscope [60].
The resulting log and tree files were then combined using LogCombiner.
The tree files were combined after a burnin of 100 trees for each run.
The phylogenetic tree files were visualized using Hypertree [41] and Treeview X software (http://darwin.zoology.gla.ac.uk/rpage/treeviewx/).gla.ac.uk/rpage/treeviewx/
The chronological tree files were analyzed and visualized using TreeAnnotator 1.5.3 [57] and FigTree 1.3.1 (http://tree.bio.ed.ac.uk/software/figtree/).ac.uk/software/figtree/
Branch lengths were automatically extracted from the tree files using the newick tools 0.1 software package [27].
Tree files are available on request.
