PhyloGibbs-MP (version 2.0)

UPDATE (Dec 19, 2007): Fixed bug where not specifying -n caused crash.
UPDATE (June 30, 2008): Uploaded nearly-final version, with minor bugfixes from previous version.
UPDATE (April 30, 2010): Belatedly uploaded final version (2.0), with minor bugfixes from previous version.
UPDATE (November 30, 2010): Belatedly uploaded binaries for linux and windows.

PhyloGibbs is a motif finder to find binding sites for transcription factors in cis-regulatory sequences of DNA.

PhyloGibbs-MP is a new version, which is now feature-complete and mostly bug-free. (This is a late beta version; the final version will be released Real Soon Now.)

REFERENCE: Rahul Siddharthan, "PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling", PLoS Comput Biol 4(8): e1000156 (2008) (link) (supporting data)

PhyloGibbs-1.0 is now deprecated, and I will upload binaries for PhyloGibbs-MP soon (user-contributed binaries are welcome.) The new program does almost everything PhyloGibbs-1.0 did (a few obscure options have been removed). New features include:

PhyloGibbs-MP 2.0 is now available. It contains only minor bugfixes from the previous version (of June 30, 2008).

The code

Source code is here.
Linux static binary (32-bit x86) here (see README file inside tarball)
Linux static binary (64-bit AMD64) here (see README file inside tarball)
Windows binary here (compiled under Cygwin on Windows Vista; see README file inside the zip archive).

For historical reasons, source code of June 30, 2008 (used for benchmarks in the paper) is here. (No binaries yet.)


Rahul Siddharthan
(Return to PhyloGibbs-1.0 page)