PHYLOCLUS

PHYLOCLUS is a suite of perl programs for clustering co-regulated genes based on phylogenetically discovered transcription factor binding motifs.

The program is described in the manuscript:

S.T. Jensen, L. Shen, and J.S. Liu (2005). Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes. Submitted to Bioinformatics.

PHYLOCLUS PROGRAM

Program: phyloclus.tgz

Readme file: PHYLOCLUS_README

SUPPLEMENTARY MATERIALS

Supplementary Document: jensenshenliu.supmaterials.pdf

Algorithm Supplement: algorithmsupplement.pdf

Clustering Results:

Studyset Independent-Block Fixed-Width Best Clusters

Studyset Independent-Block Variable-Width Best Clusters

Studyset Joint-Block Fixed-Width Best Clusters

Genome Independent-Block Fixed-Width Best Clusters

Genome Independent-Block Variable-Width Best Clusters

Genome Joint-Block Fixed-Width Best Clusters

CONTACT INFORMATION

Shane T. Jensen	stjensen at wharton.upenn.edu
Lei Shen	lshen at bioinfo.stat.harvard.edu
Jun S. Liu	jliu at bioinfo.stat.harvard.edu

Studyset	Independent-Block Fixed-Width	Best Clusters
Studyset	Independent-Block Variable-Width	Best Clusters
Studyset	Joint-Block Fixed-Width	Best Clusters
Genome	Independent-Block Fixed-Width	Best Clusters
Genome	Independent-Block Variable-Width	Best Clusters
Genome	Joint-Block Fixed-Width	Best Clusters