RASER

About
Download
Citation
Contact

The RAte Shift EstimatoR

About

RASER is a likelihood based method for testing and detecting site-specific evolutionary rate shifts.
Given a multiple sequence alignment (MSA) and a phylogenetic tree, the program determines:
(a) Whether or not site-specific rate shifts characterize the evolution of a protein, and
(b) If so, points to the specific sites and lineages in which these shifts have most likely occurred.

Download

(Current version is 2.0)

Windows executable: raser.exe
Linux executable: raser
Source code (C++): raser.v2.0.tar.gz
Manual: RASER_Manual.docx, RASER_Manual.doc, RASER_Manual.pdf
Example parameters files (see manual):
raser.params, null.params, onlyPrintNodesNames.params, raser.stochasticMapping.params, raser.allOptions.params.

Citation

Penn O, Stern A, Rubinstein ND, Dutheil J, Bacharach E, Galtier N., Pupko T. 2008.
Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes.
PLoS Computational Biology 4(11): e1000214. Full text

Contact

For any questions or suggestions please contact Osnat Penn or Adi Stern.