Ergatis, from TIGR, is a genome annotation pipeline platform: http://ergatis.sourceforge.net/.
EvoPrinter, from the National Institute of Neurological Disorders and Stroke, is a comparative genomics tool that enables users to identify conserved DNA sequences in the context of a single species of interest: http://evoprinter.ninds.nih.gov/.
ExonScan, from the Massachusetts Institute of Technology, predicts splice sites for vertebrate genomes: http://genes.mit.edu/exonscan/.
Flash GViewer, from the Medical College of Wisconsin, is a customizable Flash movie that can be inserted into a web page to display chromosomes in a genome along with the locations of individual features on the chromosomes: http://www.gmod.org/FlashGViewer/.
Galaxy, from the Penn State Center for Comparative Genomics and Bioinformatics, enables developers to easily create an HTML user interface for their data analysis tools: http://g2.bx.psu.edu.
GeneSeer, from Cold Spring Harbor Lab, is a name-translation database that enables researchers to reconcile gene names from different species: http://geneseer.cshl.org/scripts/main.pl.
HapMart, from Cold Spring Harbor Laboratory, is a data-mining interface for data from the International HapMap project: http://hapmart.hapmap.org/BioMart/martview.
NestedMICA, from the Wellcome Trust Sanger Institute, is a motif finder with applications in finding candidate transcription factor binding sites: http://www.sanger.ac.uk/Software/analysis/nmica/.
ProteinPathGrep, from Princeton University, finds all paths in a protein-protein interaction network that match a given pattern: http://www.cs.princeton.edu/~ebanks/pgrep/index.html.
Sombrero, from the National University of Ireland, Galway, finds transcription factor binding sites by using a self-organizing map to find overrepresented motifs in a set of DNA sequences: http://bioinf.nuigalway.ie/sombrero/download.html.
Sybil, from the Institute for Genomic Research, offers comparative analysis tools for TIGR's Pathema database of pathogenic genome sequences: http://sybil.sourceforge.net/.
TreeFam, (tree families database), from the Wellcome Trust Sanger Institute, is a database of phylogenetic trees of animal genes: http://www.treefam.org/.
Ulysses, from the University of British Columbia, can project molecular interaction networks across species in order to annotate human genes based on gene interactions in model organisms: http://www.cisreg.ca:8080/ulysses/.