Software no longer in active development

The first publicly available, standalone genome sequence scaffolding program. It orders and orients contigs into scaffolds based on various types of linking information.

a computational screening test that takes the raw DNA sequence data from a whole-genome sequence of an individual human and tests for each of 68 known mutations in the BRCA1 and BRCA2 genes.

(New in Nov 2008) Highly Sensitive Short Read mapping with MapReduce. CloudBurst uses Hadoop - an open source version of Google's parallel computing software MapReduce - to efficiently parallelize the short read mapping problem to dozens or hundreds of computers. This enables CloudBurst to execute highly sensitive read mappings with any number of mutations or indels.

(New in Nov 2009) Crossbow is a scalable software pipeline for whole genome resequencing analysis. It combines Bowtie, an ultrafast and memory efficient short read aligner, and SoapSNP, an accurate genotyper, within Hadoop to distribute and accelerate the computation with many nodes. The pipeline can accurately analyze over 35x coverage of a human genome in one day on a 10-node local cluster, or in 3 hours for about $100 using a 40-node, 320-core cluster rented from Amazon's EC2 utility computing service.

(New in September 2009) A transcript assembler and abundance estimator for RNA-Seq

A motif finder based on Gibbs sampling that can find ribosome binding sites, exon splicing enhancers, or regulatory sites.

a Phylogenetic Generalized Hidden Markov Model for finding alternatively spliced exons.

A vector trimmer capable of accurately trimming vector from shotgun reads without prior knowledge of the vector sequence. Figaro statistically models short oligo-nucleotide frequencies in order to infer which oligos are associated vector sequence.

A fast accurate software to increase the length of reads by overlapping and merging mate pairs from fragments shorter than twice the length of reads.

a program for analysis of microarray data including rank scores for over-representation of particular functions and categories

a fast system for detecting splice sites in genomic DNA of various eukaryotes.

a generalized HMM for eukaryotic gene finding, with a design similar to Genscan. Written and maintained by Bill Majoros, now at Duke University.

GiRaF is a computational tool for identification of reassortments in influenza viruses from sequence databases of isolates.

a system that uses interpolated Markov models to find genes in microbial DNA. Used to annotate hundreds (possibly thousands) of bacterial, archaeal, and viral genomes. Current version is 3.02.

a Generalized Hidden Markov Model gene-finder which makes use of the techniques implemented previously by GlimmerM.

A visual analytics tool for genome assembly analysis and validation, designed to aid in identifying and correcting assembly errors. All levels of the assembly data hierarchy are made accessible to users, along with summary statistics and common assembly metrics. A ranking component guides investigation towards likely mis-assemblies or interesting features to support the task at hand. Can be used to interactively analyze assemblies from many popular assemblers on your desktop computer. See the journal paper here.

(previously called Combiner),a program that predicts gene models using the output from other annotation software. It uses a statistical algorithm to identify patterns of evidence corresponding to gene models.

MetaPath can identify differentially abundant pathways in metagenomic data-sets, relying on a combination of metagenomic sequence data and prior metabolic pathway knowledge.

Metastats is software for detecting differentially abundant features in metagenomic case/control studies. It is the first tool developed in the context of metagenomic data comprising multiple samples, and relies on a non-parametric t-test. This software is no longer current, not recommended for use, and is not being provided anymore. Newer tools exist in this space, such as metagenomeseq, corncob, and others.

A small, lightweight assembler for small jobs such as assembling a viral genome, assembling a set of reads that match a single gene, or other tasks that don't require the complex infrastructure of a large-genome assembler.

a system for aligning whole genomes, chromosomes, and other very long DNA sequences. New (May 2008): see how to use MUMmer to align Solexa reads to the human genome.

High throughput sequence alignmentusing Graphics Processing Units (GPUs). Uses a technique called general-purpose GPU programming (GPGPU programming) to harness the extreme parallelism of GPUs for non-graphics tasks. In this application, hundreds of query sequences are simultaneously aligned to a reference sequence, creating an order of magnitude speed up over the same alignmenton the CPU.

Software and a database of operons covering a large number of prokaryotic genomes. Described in M. Pertea et al., Nucl. Acids Res 37 (2009), D479-D482.

PanArray is an oligonucleotide probe selection algorithm for tiling multiple genome sequences using a minimal number of probes. It is capable of fully tiling all genomes of a species on a single microarray chip. These unique pan-genome tiling arrays provide maximum flexibility for the analysis of both known and uncharacterized strains.

A one-stop system for taxonomically classifying metagenomic short reads.

A software package to detect and correct substitution sequencing errors in WGS data sets with deep coverage.

an older system for finding and characterizing repetitive sequences in complete and partial genomes.

A tool for unsupervised clustering of metagenomic sequences using interpolated Markov models.

an online tool for identifying exon splicing enhancers (ESEs) in Arabidopsis and Drosophila.

An efficient program to align cDNA sequences (or ESTs)to genomic sequences, specifically designed for cross-species alignment.

A highly accurate program that finds rho-independent transcription terminators in bacterial genomes. The site includes a database with pre-computed predictions for hundreds of species.