PhyloGibbs

NEW A significant enhancement, PhyloGibbs-MP, is now available. It is in late beta form, but almost final, and PhyloGibbs-1.0 (the version below, which was released with the original paper) is now deprecated. Please consider using PhyloGibbs-MP instead.

The original version of PhyloGibbs is being maintained at Erik van Nimwegen's group in Basel and is available here. It, too, differs in some ways from PhyloGibbs-1.0. A web interface is available here.


PhyloGibbs is a motif finder to find binding sites for transcription factors in cis-regulatory sequences of DNA. It is based on the Gibbs sampling algorithm, but with the following enhancements:

References:

Read the phylogibbs(1) manpage on basic usage of the program, and the phylogibbs_algorithm(7) manpage describing the algorithm.

The code:
The final (version 1.0) version of PhyloGibbs is released now. A webserver where one can submit PhyloGibbs jobs is also planned. The last feature-complete snapshot on this page (November 15, 2005) had a small bug in string-handling when parsing the "-L" option, which apparently showed up only on very new linux systems: this is the only fix in 1.0, but if "-L" works for you in the 20051115 version, you don't need to upgrade. Further development continues and will be made available in later versions.

(Changes from earlier snapshot of July 28: a change in the -L syntax to conform with the standard Newick syntax; new options -M, -x, -y (not described in paper; see manpage).

For Unix manual pages and examples, download the source distribution.

To know more, contact me or one of the other authors.

The authors of PhyloGibbs are:
Rahul Siddharthan, The Institute of Mathematical Sciences
     (much of this work was done at The Rockefeller University)
Eric D. Siggia, The Rockefeller University
Erik van Nimwegen, Biozentrum, University of Basel