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:
- A significant speed improvement (it runs about 10x faster, without
sacrificing much accuracy)
- Instead of picking a fixed prior expected number of binding sites, one now chooses a prior density: this density applies to each sequence and is independent of the relatedness of sequences. See the -p and -n options.
- One can restrict predictions to an unspecified subregion of the given input sequence, for example when one is unsure of the location of a cis-regulatory module. In other words, PhyloGibbs-MP can predict CRMs simultaneously with binding sites. See the -l and -n options.
- One can predict motifs that discriminate between two or more groups of differently regulated genes (that is, motifs that appear preferentially in one group). See the -d option.
- The implementation of the -M option (informative priors) has been changed.
- Optionally, PhyloGibbs-MP outputs annotations that can be read by the Generic Genome Browser. See the -g option.
- Many other details have changed: please read the manpages carefully!
PhyloGibbs-MP 2.0 is now available. It contains only minor bugfixes from the previous version (of June 30, 2008).
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.)
(Return to PhyloGibbs-1.0 page)