EvolSimulator: A simulation test bed for gene and genome evolution
Robert G. Beiko and Robert L. Charlebois
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
on any UNIX system with gcc/g++ installed.
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.
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
Version 2.1.0 - Source code, makefile, and config
Version 2.0.4 - Source code, makefile, config and manual
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.
Contact the authors: Robert G. Beiko or
© 2005-2006 Robert G. Beiko