We strive for

• Methodologial Transparency
• Biological Interpretability
• Statistical Rigor

in development of our methods. The following software is available:

Quantitative Enrichment of Sequence Tags: QuEST (new as of 3/11/08)

QuEST works with ChIP-seq data. It finds sites in the genome that have enrichment signals, and are therefore candidates for transcription factor binding sites. A paper has been submitted.

Genomic Evolutionary Rate Profiling: GERP (updated 2/11/08)

GERP is a framework for constrained element identification that utilizes quantification of nucleotide substitution events within a multiple sequence alignment. GERP is published (pdf).

Multivariate Analysis of Protein Polymorphism: MAPP (updated 6/28/05)

MAPP quantifies physicochemical constraint violation of all possible amino acid substitutions, using a multiple alignment of protein sequences related by a phylogenetic tree. MAPP is published (pdf).

Application for Browsing Constraints: ABC (updated 6/28/05)

The ABC is Java software for the exploration of multiple sequence alignments and data typically associated with genomic alignments. The ABC is published (pdf).

Branch Manager: BM (updated 12/28/06)

The BM reads a phylogenetic tree with branch lengths and outputs a weight for each sequence that describes its contribution to the total information captured by the tree. BM is published (pdf). Download the zipped BM folder.

Marker (zip of jar and documentation; updated 6/28/05)

A super-lightweight Java program for interactive scoring of medium-sized features in large image files, as illustrated by the excerpt from a large image on the right. Unpublished.