Sequence Alignment

Sim4
Clustal
ClustalW
MSA
PiP Maker
Sequence Logos
SAM
DNA Dot plots

Phylogeny

Phylip -- J. Felsenstein, UW
PAUP
Joe Felsenstein's Phylogeny Links
ClustalW
TreeView

Sequence Assembly

ARACHNE
Phrap
TIGR Assembler

Motif Sampling

METAMEME

RNA Secondary Structure

FOLDALIGN
dynalign

Repetitive Elements

RepBase

Gene Prediction

Genie
Twinscan
HMM Gene
Grail
GenScan
GeneWise

Commercial Products

Informax
(Vector NTI, Expression NTI)
GCG
Staden Package
DNA Star

Sequencing Centers

Baylor College of Medicine
Stanford Human Genome Center
DOE Joint Genome Institute
Washington University GSC
Whitehead Institute MIT
Sanger Centre