Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

Abstract

Motivation: Seq-Gen is a program that will simulate the evolution of nucleotide sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. Nucleotide frequencies and other parameters of the model may be given and site-specific rate heterogeneity can also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus, large sets of replicate simulations can be easily created. This can be used to test phylogenetic hypotheses using the parametric bootstrap.

Availability: Seq-Gen can be obtained by WWW from http://evolve.zoo.ox.ac.uk/Seq-Gen/seq-gen.html or by FTP from ftp://evolve.zoo.ox.ac.uk/packages/Seq-Gen/. The package includes the source code, manual and example files. An Apple Macintosh version is available from the same sites.