Genome Servers

BDGP	http://www.fruitfly.org/
Ensembl	http://www.ensembl.org/
ExoFish	http://www.genoscope.cns.fr/externe/tetraodon/
FlyBase	http://flybase.bio.indiana.edu/
GRAMENE	http://www.gramene.org/
HGSC_Baylor	http://www.hgsc.bcm.tmc.edu/
JGI	http://genome.jgi-psf.org/
MGD	http://www.informatics.jax.org/
NCBI	http://www.ncbi.nlm.nih.gov/
NISC	http://www.nisc.nih.gov/
Rat Genome	http://www.rgd.mcw.edu/
Sanger	http://www.sanger.ac.uk/
SGD	http://genome-www.stanford.edu/Saccharomyces/
TAIR	http://www.arabidopsis.org/
TIGR	http://www.tigr.org/
UCSC	http://www.genome.ucsc.edu/
Wormbase	http://www.wormbase.org/

Genome Comparative Analysis Tools

Genomic Sequences from:

ECR Browser	http://ecrbrowser.dcode.org/	human/mouse/fugu
GALA	http://globin.cse.psu.edu/	human/mouse
Penn State	http://bio.cse.psu.edu/genome/hummus/	human/mouse
UCSC	http://www.genome.ucsc.edu/	human/mouse/rat
VISTA	http://pipeline.lbl.gov/	human/mouse/rat

Alignment Tools

Alfresco	http://www.sanger.ac.uk/Software/Alfresco/
AVID	http://baboon.math.berkeley.edu/mavid/
BALSA	http://bayesweb.wadsworth.org/balsa/balsa.html
BLAST	http://www.ncbi.nlm.nih.gov/BLAST/
Blast2Sequences	http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html
BLAT	http://genome.ucsc.edu/cgi-bin/hgBlat
BLOCKS	http://blocks.fhcrc.org/
ClustalW	http://www.ebi.ac.uk/clustalw/
DIALIGN2	http://www.gsf.de/biodv/dialign.html
EMBOSS	http://www.ebi.ac.uk/emboss/align/
GLASS	http://glass.lcs.mit.edu/
LAGAN	http://lagan.stanford.edu/
LALIGN	http://www.ch.embnet.org/software/LALIGN_form.html
MUMmer	http://www.tigr.org/software/mummer/
Pattern Hunter	http://www.bioinformaticssolutions.com/products/ph.php
Pfam	http://www.sanger.ac.uk/Software/Pfam/
PipMaker	http://bio.cse.psu.edu/pipmaker/
Poa	http://www.bioinformatics.ucla.edu/poa/POA_Online/Align.html
SAM	http://www.cse.ucsc.edu/research/compbio/sam.html
SSAHA	http://www.sanger.ac.uk/Software/analysis/SSAHA/
SSEARCH	http://www.biology.wustl.edu/gcg/ssearch.html
SynPlot	http://www.sanger.ac.uk/Users/jgrg/SynPlot
Tcoffee	http://www.ch.embnet.org/software/TCoffee.html
VISTA	http://www-gsd.lbl.gov/VISTA/index.html
WUBlast2	http://www.ebi.ac.uk/blast2/

Transcription Factor Binding Site Analysis

CIS-ANALYST	http://rana.lbl.gov/cis-analyst/
CONSITE	http://forkhead.cgr.ki.se/cgi-bin/consite
RVISTA	http://rvista.dcode.org/
TESS	http://www.cbil.upenn.edu/tess/
TRANSFAC	http://www.biobase.de/

Phylogenetic Footprinting

FootPrinter	http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/FootPrinterInput2.pl
TRES	http://bioportal.bic.nus.edu.sg/tres/
EShadow	http://eshadow.dcode.org/

Pattern Finding

AlignACE	http://atlas.med.harvard.edu/
ANN-Spec	http://www.cbs.dtu.dk/services/DNAarray/ann-spec.html
CONSENSUS	http://www.bork.embl-heidelberg.de/Alignment/consensus.html
MEME	http://meme.sdsc.edu/meme/website/intro.html

Clustering of TFBS or Motifs

CIS-ANALYST	http://rana.lbl.gov/cis-analyst/
Cister	http://zlab.bu.edu/~mfrith/cister.shtml
GALA	http://gala.cse.psu.edu/
RVISTA	http://rvista.dcode.org/
TFCLUSTER	http://stateslab.bioinformatics.med.umich.edu/service/tfcluster/
TraFaC	http://trafac.chmcc.org

Clustering of Motifs upstream of Coexpressed Genes from Microarray Data

BioProspector	http://bioprospector.stanford.edu/
CREME	http://creme.dcode.org/

Primer Design
CODEHOP (degenerate primers)	http://blocks.fhcrc.org/codehop.html
Primer3	http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi
PrimerX (mutagenic primers)	http://bioinformatics.org/primerx/

Molecular Biology
ORF	http://www.ncbi.nlm.nih.gov/gorf/gorf.html
Reverse Complement	http://bioinformatics.org/sms/rev_comp.html
Restriction Enzymes (NEB)	http://tools.neb.com/NEBcutter2/index.php
EST Assembler	http://bio.ifom-firc.it/ASSEMBLY/assemble.html

Thanks to Gabby for putting together this list.