SEQ-GEN - AN APPLICATION FOR THE MONTE-CARLO SIMULATION OF DNA-SEQUENCE EVOLUTION ALONG PHYLOGENETIC FREES

Motivation: Seq-Gen is a program that will simulate the evolution of n ucleotide sequences along a phylogeny, using common models of the subs titution process. A range of models of molecular evolution are impleme nted, including the general reversible model. Nucleotide frequencies a nd other parameters of the model may be given and site-specific rate h eterogeneity 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 dat a sets for each tree. Thus, large sets of replicate simulations can be easily created. This can be used to test phylogenetic hypotheses usin g the parametric bootstrap. Availability: Seq-Gen can be obtained by W WW 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.