Links: Tools, Software, and Information

PHYML "fast and accurate heuristic for estimating maximum likelihood phylogenies. Large DNA and protein sequences data sets can be analysed under a broad range of substitution models."

Splitstree produces network as well as tree analysis of phylogenetic (and other) data.

MEGA a versatile, user-friendly program that does phylogenetic analysis and bootstrapping. Windows.

Tree-Puzzle "a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood." Windows, UNIX, Mac, VMS.

TreeFinder A very fast Maximum Likelihood tree program; supports six popular models of sequence evolution. Windows, UNIX, Mac.

HyPhy Another program for maximum-likelihood trees; very flexible and comes with its own programmable interface. Windows, UNIX, Mac.

DataMonkey Detects positive and negative selection on individual amino acid sites by counting the number of nonsynonymous and synonymous substitutions; runs a Single Likelihood Ancestor Counting (SLAC) analysis, a heavily modified and efficiently implemented version of the Suzuki-Gojobori method to identify positively and negatively selected sites.

Treeview displays treefiles; more flexible and easy to use than Drawtree/Drawgram. Windows, Mac, Linux/UNIX.

Modeltest "helps a user to choose the model of DNA substitution that best fits his/her data, among 56 possible models." Windows, UNIX, Mac.

Phylogenetic Analysis A comprehensive list of programs for creating phylogenetic trees, maintained by Joe Felsenstein at the University of Washington.

BEAST Bayesian Evolutionary Analysis Sampling Trees: a cross-platform program for Bayesian MCMC analysis of sequences; can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.

BioEdit is a full-featured alignment editor for nucleotides and amino acids; comes with built-in alignment and tree-building programs.

Hidden Markov Models the HMMER programs developed by Sean Eddy. We now use HMMs to dynamically generate alignments for our search interface.

CLUSTALX CLUSTALX is distibuted as executables for DOS/Windows, Mac and UNIX operating systems.

Se-Al Se-Al is a user-friendly alignment editor; only available for Mac.

Multiple Sequence Alignment a collection of alignment programs such as CLUSTALW, for aligning nucleic acid or amino acid sequences. Maintained by the Department of Genetics at the University of Washington, Seattle.

SAM: Sequence Alignment and Modeling Programs Similar to HMMER, this is a package of tools for building and using Hidden Markov Models of sequence alignments; includes tool to convert between SAM and HMMER formats.

READSEQ allows you to convert sequences to and from 15 different formats.

Arlequin cross-platform Java program for population genetic analysis; takes sequence, RFLP, microsatellite, and allele frequency data; calculates measures of diversity, provides tests for linkage and Hardy-Weinberg disequilibrium, etc.

Crann A program that can test for adaptive evolution, or mutational evidence of selection pressure. Fast, reliable, and easy to use.

Simplot tool for recombination analysis by Stuart Ray at Johns Hopkins University; does both similarity plots and bootscan analysis; the most widely used for recombination analysis in HIV research.

BankIt and Sequin are tools for sequence submission to GenBank (NCBI). Use BankIt if you have a few sequences; use Sequin for larger or more complicated sets of sequences.

Oxford Evolutionary Biology Group software contains many high-quality programs.

Edinburgh University Molcular evolution, phylogenetics and epidemiology software contains many high-quality programs, among them Se-Al (multiple sequence alignment program) and many Monte Carlo programs to simulate tree and sequence evolution.

Protein prediction at Columbia University. A very nice tool for protein structure prediction and several other analyses.

Genetic Data Environment An integrated Linux environment for bioinformatics and evolutionary analysis; see also MacGDE for MacOS X.

Hyperback A software package for the study of levels, contexts, and patterns of APOBEC-mediated hypermutation in HIV

Mullins Computational Biology Tools home to a suite of programs developed at the University of Washington in the Mullins laboratory for analysis of HIV (and other) sequences, including diversity assessment tools, a method for rooting a tree in a central position, and other useful scripts and software.

NCBI HIV Subtyping tool performs subtyping of a new sequence by comparing it to a set of reference sequences using BLAST.

REGA Viral Subtyping BioAfrica viral subtyping tools, which use phylogenetic methods to identify the subtype. Sequences are analyzed for recombination using bootscanning.

Prediction of coreceptor usage for HIV-1 tool at UCSD.

WebPSSM, a web based tool for prediction of R5/X4 phenotype based on V3 sequences.

NIH AIDS Reagent Program provides biological and chemical materials for study of HIV

NIBSC AIDS Reagent Program a repository for HIV/AIDS reagents in the UK

Stanford HIV RT/protease database a searchable and very useful tool for drug-associated mutations

HIV-1, Human Protein Interaction Database an NCBI site summarizing all known interactions of HIV-1 proteins with host cell proteins, other HIV-1 proteins, or proteins from disease organisms associated with HIV/AIDS

AIDS Information at the National Institutes of Health (NIH), maintained by the National Institute of Allergy and Infectious Diseases (NIAID)

MedWeb a huge collection of links to AIDS-and HIV-related websites, maintained at Emory University

AIDScience the HIV prevention and vaccine research site of the American Association for the Advancement of Science

The Body a complete HIV/AIDS resource, including a Glossary of HIV/AIDS terminology

UNAIDS the United Nations Global Programme on AIDS

IAVI the International AIDS Vaccine Initiative

Pediatric AIDS Foundation

Johns Hopkins AIDS service

Harvard AIDS Institute

AEGiS AIDS Education Global Information System

AVAC AIDS Vaccine Advocacy Coalition

New Mexico AIDS Infonet

AIDScience Archive HIV prevention and vaccine research site of the AAAS

International AIDS Vaccine Initiative

Molecular Immunology a tutorial for human immunogenetics and immunobiology

AIDSTruth.org the scientific evidence for HIV/AIDS

All the Virology on the WWW links and descriptions for many science resources and websites in virology and microbiology

Critical Path image library

UNAIDS slide collection

HIV/AIDS Conferences Worldwide a current list of conferences

AIDS Conferences (The Body) coverage of past conferences and list of future conferences

CROI Conference on Retroviruses and Opportunistic Infections

HIV Dynamics & Evolution a conference promoting discussion among HIV specialists