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.

Birth-Death (Bi-De) is an application for the Apple Macintosh which simulates the growth of phylogenetic trees using various models of lineage birth and death. The trees produced are intended to be analogous to those reconstructed from molecular sequence data. The user may define a constant birth rate and death rate or a function describing how these rates vary by time or population size. Instantaneous mass extinctions can also be simulated. The package allows the tree produced to be used as a template for the simulated evolution of molecular sequence data under a range of different transition models.