Useful Resources
Joe Felsenstein's list of phylogeny programs: Here are 386 phylogeny packages and 52 free servers, all that I know about. It is an attempt to be completely comprehensive. I have not made any attempt to exclude programs that do not meet some standard of quality or importance. Updates to these pages are made roughly weekly. Here is a "waiting list" of new programs waiting to have their full entries constructed. Many of the programs in these pages are available on the web, and some of the older ones are also available from ftp server machines. ......
David Robertson's Research Group: My research is primarily focussed on bioinformatics and molecular evolution. Evolution is what explains life and its many forms, and so it is of central importance to biology. Molecular evolution is specifically the study of evolution at the molecular level from genes to genomes to systems biology, while bioinformatics is the use of computers in biological research to address analytical and theoretical questions/hypotheses. My own research particularly involves ......
Web PSSM: WebPSSM is a bioinformatic tool for predicting HIV-1 coreceptor usage from the amino acid sequence of the third variable loop (V3) of the envelope gene. ......
Geno2pheno: On submitting below a sequence containing the V3 region of the HIV-1 envelope protein gp120, you will obtain a sequence alignment to the reference strain HXB2 and a prediction whether the corresponding virus is capable of using CXCR4 as a coreceptor (R5/X4 or X4 variants) or not (R5 variants). ......
HIV database: The HIV databases contain data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials. The website also gives access to a large number of tools that can be used to analyze these data. ......
PubMed: PubMed is a service of the U.S. National Library of Medicine that includes over 18 million citations from MEDLINE and other life science journals for biomedical articles back to 1948. PubMed includes links to full text articles and other related resources.
Sun Microsystems: The developers of the Java programming language.
Andrew Rambaut's Research Group: This site is for the research, software and publications of Andrew Rambaut and members of his research group.
Java Evolutionary Biology Library: A Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees.
PAL: Phylogenetic Analysis Library: The PAL project (http://www.cebl.auckland.ac.nz/pal-project) is a collaborative effort dedicated to provide a high quality Java library for use in molecular evolution and phylogenetics.

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