Computational Gene Finding (all programs are open source)

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.
TWAIN   a Generalized Pair HMM to predict genes simultaneously in two closely related eukaryotic organisms.
GlimmerHMM
a Generalized Hidden Markov Model gene-finder which makes use of the techniques implemented previously by GlimmerM.
GeneZilla
a generalized HMM for eukaryotic gene finding, with a design similar to Genscan.  Written and maintained by Bill Majoros, now at Duke University.
ExAlt
 a Phylogenetic Generalized Hidden Markov Model for finding alternatively spliced exons.
JIGSAW
 (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.
GeneSplicer
 		a fast system for detecting splice sites in genomic DNA of various eukaryotes.
PIRATE
a website collecting many links to our gene finders and others.
SIM4CC   An efficient program to align cDNA sequences (or ESTs)to genomic sequences, specifically designed for cross-species alignment.

Genome assembly and large-scale genome alignment (all programs are open source)
Mummer
 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 alignment using 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 alignment on the CPU.
AMOS Assembler project  AMOS The is a set of tools, libraries, and freestanding genome assemblers, all open source. AMOS is also an open consortium that includes TIGR, the University of Maryland, The Karolinska Institutet, and the Marine Biological Laboratory.
ABBA
  AMOS
Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly.  See the journal paper. Link for installation and more information..
AMOScmp
  AMOS
is a comparative genome assembler, which uses one genome as a reference on which to assemble another, closely related species.  See the journal paper here.
MINIMUS
 AMOS 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.
Bowtie
 (New in August 2008) An ultrafast, memory-efficient short read aligner that aligns short DNA sequences to the human genome at a rate of about 25 million reads per hour on a typical workstation with 2 GB of memory. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: 1.1 GB for the human genome.
TopHat
 (New in February 2009) A short read aligner for RNA-Seq experiments. TopHat discovers novel exon-exon splice junctions and can align millions of RNA-Seq reads to a mammalian genome per hour.
Cufflinks
 (New in September 2009) A transcript assembler and abundance estimator for RNA-Seq
BAMBUS
  bambus
the first publicly available, standalone genome sequence scaffolding program. It orders and orients contigs into scaffolds based on various types of linking information.
CloudBurst
 (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.
Hawkeye
 hawkeye
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.
AutoEditor AutoEditor
 A tool for correcting sequencing and basecaller errors using sequence assembly and chromatogram data. On average AutoEditor corrects 80% of erroneous base calls, with an accuracy of 99.99%.
Figaro
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.
Celera Assembler
A whole genome assembler originally developed at Celera Genomics for the assembly of the human genome.  CeleraAssembler is now an open-source project at SourceForge.  The code is actively maintained by researchers at CBCB and the Venter Institute (formerly known as TIGR, The Institute for Genomic Research).

Other sequence analysis tools (all programs are open source)
ELPH a motif finder that can find ribosome binding sites, exon splicing enhancers, or regulatory sites.

a program that finds rho-independent transcription terminators in bacterial genomes.
 
 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.
GeneMerge
a program for analysis of microarray data including rank scores for over-representation of particular functions and categories
SEE ESE   an online tool for identifying exon splicing enhancers (ESEs) in Arabidopsis and Drosophila.
RepeatFinder
an older system for finding and characterizing repetitive sequences in complete and partial genomes.
Metastats
Statistical methods for detecting differentially abundant features in metagenomic data.
Phymm+PhymmBL
A one-stop system for taxonomically classifying metagenomic short reads.
A collection of links to external sequence analysis programs.