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Classification Society of North America

http://www.pitt.edu/~csna/software.html

List of cluster analysis software

Genetics Software from the Slatkin Lab

http://ib.berkeley.edu/labs/slatkin/software.html

Links to sites for downloading phylogenetic software.

GenomeWeb phylogenetic analysis page

http://www.hgmp.mrc.ac.uk/GenomeWeb/phylogenetic-anal.html

http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html

Multiple Alignment Resources

Glasgow taxonomy and systematics software

http://taxonomy.zoology.gla.ac.uk/software.html

http://ftp.bio.indiana.edu/IUBio-Software+Data/molbio/evolve/

Molecular evolution software

http://ftp.bio.indiana.edu/IUBio-Software+Data/molbio/mac/

Macintosh molecular biology software

Joe Felsenstein's list of phylogeny programs

http://evolution.genetics.washington.edu/phylip/software.html

Probably the most comprehensive

Willi Hennig Society - Education

http://www.cladistics.org/education.html

Links to recent books, software, and resources.