[Rmannounce] COSEG Beta Released

[Robert Hubley]

COSEG is a program which automatically identifies repeat subfamilies 
using significant co-segregating ( 2-3 bp ) mutations.

This program is derived from three C programs and several perl scripts 
written by Alkes Price as part of an analysis of Alu elements in the 
human genome ( Whole-genome analysis of Alu repeat elements reveals 
complex evolutionary history, Alkes L. Price, Eleazar Eskin, and Pavel 
Pevzner, 2004 Genome Research ). The program was first adapted for use 
with other repeat families and then extended to support consideration of 
three co-segregating mutations using Alkes statistical model. In 2008 
with the help of Andy Siegel an alternative statistical model was 
developed and the codebase repackaged into the single source file.

The code may be downloaded from 
http://www.repeatmasker.org/COSEGDownload.html.

We appreciate user feedback on this new software package.