Genome Alignment Browsers:

• Gbrowse - 1.70 - Genomic Browsing, Generic Model Organism Database Project
  http://www.gmod.org/wiki/index.php/Gbrowse
• Staden Tools (GAP5, TGAP) - 2.0.0b2 - Alignment and Visualization for Small Data Sets, James Bonifield (initially developed by Rodger Staden), Wellcome Trust Sanger Institute
  http://sourceforge.net/projects/staden/

Genome Annotation Viewer and Editors:

• Apollo - 1.11.2 - Sequence annotation editor. Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Ricter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS, Matthews B, Prochnik SE, Smith CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME (2002). Genome Biology 2002, 3(12):research0082
  http://www.dhgp.org/current/index.html

Genomic Assembly:

• Velvet - 0.7.55 - De novo assembly of short reads, Daniel Zerbino and Ewan Birney, EMBL-EBI
  http://www.ebi.ac.uk/~zerbino/velvet/

Alignment and Polymorphism Detection:

• BFAST - 0.6.1 - Blat-like Fast Accurate Search Tool, Nils Homer, Stanley F. Nelson and Barry Merriman, University of California, Los Angeles
  http://genome.ucla.edu/bfast
• Bowtie - 0.11.3 - An ultrafast memory-efficient short read aligner, Ben Langmead and Cole Trapnell, Center for Bioinformatics and Computational Biology, University of Maryland
  http://bowtie-bio.sourceforge.net/
• MAQ - 0.7.1 - Mapping and Assembly with Quality, Heng Li, Sanger Centre
  http://maq.sourceforge.net/maq-man.shtml

Other:

• SHORE - 0.4.1 - mapping and analysis pipeline for short DNA sequences
  http://1001genomes.org/downloads/shore.html
• BioPerl - a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications
  http://www.bioperl.org/wiki/Main_Page