Phylogenetics in the Department of Computer Science and Engineering

A listserv phylogen@vm.sc.edu exists for discussion and communication among the research team. For information about listserv services at USC, go to the listserv support page. For information about the listserv and how to use it, go to the user handout page.

A local bibliography in postscript or pdf on phylogenetics and computational biology.

Some journals relevant to phylogenetics.

Laszlo Szekely's student Szilard Bokros's short quartet programs.

Joe Felsenstein's PHYLIP web page on phylogenetics at the University of Washington.

The Society of Australian Systematic Biologists

Stuart Brown at New York University

David Bader at the University of New Mexico

Paul Lewis at the University of Connecticut and at the Marine Biological Lab workshop, and software at the MBL.

The fastDNAml software at Indiana University. Another MPI version can also be downloaded. Yet another version parallelized with TreadMarks (distributed shared memory) by Denis Beaumont can also be downloaded.

Bryan Clarke's website at Nottingham, including his bibliography.

Kathy Yelick's website at Cal-Berkeley, including her paper "Parallelizing the Phylogeny Problem" with Jeff Jones.

Bernard Moret's website at New Mexico, including the GRAPPA (Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms) download.

K. Strimmer's website, the TREE-PUZZLE 5.0 code (released in October 2000), featuring a parallel computation engine based on MPI, and related papers

ClustalX and ClustalW (SGI parallel code)

MALIGN, a parsimony-based alignment program for molecular sequences.

An online program for converting acronyms into their biomedical long forms.

A link from Xizhou Feng to papers in Bayesian inference for phylogeny.