Seq-Gen is 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.

The latest version of Seq-Gen can be downloaded from:

Version History

2017-09-17 - v1.3.4

Bug fixes and FASTA output
2011-10-28 - v1.3.3

Bug fixes and an additional amino acid model (mtArt)
New features:
  • MtArt amino acid model added by Lars Jermiin.
Bugs fixed:
  • Memory allocation bugs (thanks to Graham Jones for submitting a fix)
  • Rare array overflow causing odd characters in sequence. Thanks to Howard Ross, Jeff Thorne and Michael Ott for independently spotting this error and Michael and Lars Jermiin for submitting a fix.
2005-01-07 - v1.3.2

Important bug fix related to PAM and BLOSUM amino acid models
Bugs fixed:
The PAM (Dayhoff) and Blosum matrices were interchanged so specifying one would result in the other being used instead.
2004-11-04 - v1.3.1

Important bug fix related to specifying nucleotide frequencies
Bugs fixed:
Fixed a problem where specified nucleotide frequencies were being ignored and equal frequencies were used. This problem was not in versions prior to 1.3.
2004-09-10 - v1.3

New version that can now simulate amino acid sequences.
New features:
  • Added amino acid simulation to Seq-Gen. This replaces PSeq-Gen which was not being updated but also adds a number of other amino acid models.
  • Removed the limit on tree size. The only limit now is the available memory.
  • Updated to the latest version of the MT19937 random number generator.
Bugs fixed:
Fixes a problem with reading taxon labels containing whitespace. Whitespace is now removed.
2004-05-06 - v1.2.7

New version of the Mac OS X GUI wrapper, SG Runner.
New features:
2003-12-19 - v1.2.7

Improved random number generator. New Mac OS X version.
New features:
2002-12-04 - v1.2.6

Minor update - Mac OS X compatible
New features:
  • Recompiled for native Mac OS X. The UNIX version can also be compiled under the OS X terminal.
  • Improved resolution of the automatic seeding of the random number generator by adding some milliseconds to it. Thus runs of Seq-Gen that are less than a second apart will have different seeds. This probably only matters on UNIX machines using scripts to do multiple (short) runs.
Andrew Rambaut, 2007