PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees.

Abstract

PSeq-Gen will simulate the evolution of protein sequences along evolutionary trees following the procedures previously reported for the DNA sequence simulator Seq-Gen (Sequence-Generator, Rambaut and Grassly, 1997). Statis-tics calculated from these sequences can be used to give expectations under specific null hypotheses of protein evolution. This Monte Carlo simulation approach to testing hypotheses is often termed 'parametric bootstrapping' (see, for example, Efron, 1985; Huelsenbeck et al., 19%; Huelsenbeck and Rannala, 1997), and has many powerful applications, such as testing the molecular clock (Goldman, 1993), detecting recombination (Grassly and Holmes, 1997), and evaluating competing phylogenetic hypotheses (Hillis et al., 19%). Three are mitochondrial each