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UniPeak is a multisample ChIP-seq peak caller. UniPeak is published (pdf).

Quantitative Enrichment of Sequence Tags: QuEST
Click here for Anton Valouev's QuEST site
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. QuEST is published (pdf).

Genomic Evolutionary Rate Profiling: GERP
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
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
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 (zip of jar and documentation)
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).

Marker (zip of jar and documentation)
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 Unpublished.