EvolSimulator: A simulation test bed for gene and genome evolution

Robert G. Beiko and Robert L. Charlebois

Overview

EvolSimulator is a program that allows the simulation of evolution at the level of genes, gene families, and whole genomes. It was designed with the goal of investigating evolutionary phenomena like biased mutation regimes in different lineages, complicated patterns of selective pressure across sequences, and the confounding effects of paralogy and lateral genetic transfer.

Implementation and Building

EvolSimulator is implemented in C++ and released under the GNU GPL. To install EvolSimulator, you will need to obtain the (free) Boost library from www.boost.org . There is no need to "install" the library; just untar/unzip the downloaded file, then adjust the -I option within EvolSimulator's makefile to point to the folder containing "boost". See the supplied makefile for an example. If you have any trouble compiling the source code, or if you would prefer a ready-made executable for your system (assuming it's not too exotic a system...), please contact us. Once the Boost library is in place, and you have edited the makefile to point to it, just type

make

on any UNIX system with gcc/g++ installed.

Current Version

The current version of EvolSimulator is 2.1.0, which introduces a new definition of amino acid change. Previous versions can be accessed at the bottom of this page.

Download EvolSimulator

Just the manual

EvolSimulator manual (version 2.1.0)

Sample configuration file

EvolSimulator requires a properly formatted configuration file, which defines all of the parameters for the run. You can find one with the source code release below, or on its own here.

Source code

Current version

Version 2.1.0 - Source code, makefile, and config

Older releases

Version 2.0.4 - Source code, makefile, config and manual

Citing EvolSimulator

The current citation for EvolSimulator is:

Beiko, R.G. and Charlebois, R.L. (2007). A simulation test bed for hypotheses of genome evolution. Bioinformatics 23:825-831.