StepBrothers: The Brothers Have Evolved
Overview
StepBrothers is implementation of the Random Tips model. It is a descendant of the DualBrothers model developed by Minin et. al. The random tips model adopts the use of a single phylogenetic tree with a random number of tips rather than multiple trees at different time points. Its advantages include more plausible assumptions regarding the evolutionary process and joint analyses of recombinants. The random tips model also allows dating information to be obtained.
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Installation Instructions (UNIX)
- Please see documentation.
Change log
Version 1.0.1 Updated Nov 12, 2006
- Fixed formatting error in StepBreakpoints.
- Changed the tgz archive so it unpacks into a directory.
References
- Bloomquist EW, Dorman KS, Suchard MA.
The (evil) stepbrothers: inferring partially shared ancestries among recombinant viral sequences
Biostatistics, Sumitted, 2007.
- Minin VN, Dorman KS, Suchard MA.
Dual
multiple change-point model leads to more accurate recombination
detection,
Bioinformatics, 21:3034-3042, 2005.
- Suchard MA, Weiss RE, Dorman KS and Sinsheimer JS.
Inferring spatial
phylogenetic variation along nucleotide sequences:
a multiple change-point model,
Journal of the American Statistical Association
98:427-437, 2003.
- Suchard MA, Weiss RE, Dorman KS and Sinsheimer JS.
Oh brother,
where art thou? a Bayes factor test for recombination
with uncertain heritage,
Systematic Biology 51:715-728, 2002.