Bootstrap Hypothesis Testing using BootHyp

Tim Carr, Kevin O'Neil, and Donovan Bailey


BootHyp is a package of six small programs designed to be used in conjunction with the phylogenetics programs PHYLIP and PAUP* (and perhaps others).  The package facilitates the use of bootstrap procedures to conduct statistical hypothesis tests comparing rates of molecular evolution (branch lengths) on a phylogenetic tree/gene genealogy.  The software was originally developed to facilitate testing of nrDNA functionality according to Bailey et al. 2004.  However, given  a phylogenetic tree, bootstrap hypothesis testing may be used to answer a variety of questions about evolutionary rates:  Do rates of evolution along particular branches of an evolutionary tree differ among genes, gene partitions (gene regions), or codon positions?  Do rates of evolution in one sister lineage differ from those in another?  Do rates of evolution along ancestral branches differ from those along descendant branches?   Thus, bootstrap hypothesis testing will be useful whenever questions of evolutionary rate are of interest (e.g., in detecting pseudogenes, detecting the signature of natural selection, investigating the presence of a molecular clock, etc.).  It should be most applicable for molecular sequence data, but, at least theoretically, it could be used on any sort of data meeting the requirements for phylogeny reconstruction.

(Note: these are draft programs, use at your own risk - updated versions added April 2006)

BootHyp - Download Zipped File with User's Manual and associated programs