Seq-Gen

Seq-Gen was developed to be a program that will simulate the evolution of nucleotide or amino acid 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. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may 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. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution.

Seq-Gen is a command-line controlled program written in ANSI C. It should be easily compiled and run on any UNIX system or workstation. This paper describes the use of Seq-Gen on a UNIX machine. The application requires an amount of memory proportional to the size of each simulated sequence data set.

To run Seq-Gen you type:

seq-gen [parameters] < [trees] > [sequences]

where [parameters] are the parameters for the program (described below), [trees] is the tree file and [sequences] is the name of the file that will contain the simulated sequences. The tree file must contain one or more trees in PHYLIP format.

The sequences produced by Seq-Gen are written to the standard output (and can thus redirected to the output file using > [filename]). Other information and results are written to the standard error and thus will appear on the screen.