Argo, from the Broad Institute, is a tool for visualizing and manually annotating whole genomes: http://www.broad.mit.edu/annotation/argo/.
BOX-C (Blast Organism Cross-Comparison), from Hiram College, is a sequence gap closure method that aligns contigs through comparison to the NCBI non-redundant database: http://hgi.hiram.edu/boxc/.
Chisel, from Argonne National Laboratory, clusters protein sequences that are closely related in terms of homology and function: http://compbio.mcs.anl.gov/CHISEL/.
MaGe (Magnifying Genomes), from Genoscope, is a software system for computational and manual microbial genome annotation: http://www.genoscope.cns.fr/agc/mage/wwwpkgdb/index.php.
MANATEE (Manual Annotation Tool, Etc., Etc.), from TIGR, genome annotation tool that can view, modify, and store annotation for prokaryotic and eukaryotic genomes: http://manatee.sourceforge.net/.
PASA (Program to Assemble Sliced Alignments), from TIGR, is an automated system for genome annotation: http://www.tigr.org/tdb/e2k1/ath1/pasa_annot_updates/pasa_annot_updates.shtml.
Pathema, from TIGR, is a pathogen database funded by the NIAID’s BRC program: http://www.tigr.org/pathema/.
Picky, from Iowa State University, is an oligo microarray design program that identifies probes that are unique and specific to input sequences: http://www.complex.iastate.edu/download/Picky/index.html.
Puma2, from Argonne National Laboratory, is an updated version of ANL’s Puma database and bioinformatics suite for comparative analysis of genomes and metabolic networks (still in beta): http://compbio.mcs.anl.gov/puma2/cgi-bin/index.cgi.
SNP-PHAGE (Single Nucleotide Polymorphism Discovery Pipeline for Haplotype Analysis and Genbank Submissions), from USDA, is a tool for polymorphism discovery: http://snp-phage.binf.gmu.edu/.
WebGestalt, from Oak Ridge National Laboratory, is a genomic analysis toolkit that incorporates information from different public resources: http://genereg.ornl.gov/webgestalt/.