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UCSC Genome Browser
UCSC Archaeal Genome Browser

R and Bioconductor Projects

multtest package (multiple hypothesis testing)
hopach package (clustering)
Rphast package (phylogenetic analysis with space/time models) Coming soon!

PAMSIL stand alone C program (clustering)

DLESS (detection of lineage-specific selection)
available in the PHAST package developed by Adam Siepel