Seq-Gen
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:
https://github.com/rambaut/Seq-Gen/releases/latest.
Version History
- MtArt amino acid model added by Lars Jermiin.
- 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.
- 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.
- Improved the random number generator - now uses the Mersenne Twister (see http://www.math.keio.ac.jp/~matumoto/emt.html).
- Mac OS X version now includes a user interface written Thomas Wilcox.
- Improved the random number generator - now uses the Mersenne Twister (see http://www.math.keio.ac.jp/~matumoto/emt.html).
- Mac OS X version now includes a user interface written Thomas Wilcox.
- 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.