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."
RAxML is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees.
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 sites by nonsynonymous/synonymous analysis and Single Likelihood Ancestor Counting (SLAC) analysis.
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 reconstruct phylogenies and test evolutionary hypotheses without conditioning on a single tree topology.
MrBayes Bayesian Evolutionary Analysis Sampling Trees: a cross-platform program for Bayesian MCMC analysis of sequences; can reconstruct phylogenies and test evolutionary hypotheses without conditioning on a single tree topology.
Multiple Sequence Alignment
SeaView is a full-function alignment editor that can do automatic alignments and trees and allows plug-ins. Runs on most operating systems.
AliView is another nice editor that runs on modern Macs (10.9+), as well as on Linux and Windows.
Jalview is a free program for multiple sequence alignment editing, visualization and analysis.
Se-Al Se-Al is a user-friendly alignment editor, but only works on old Macs (10.6 or earlier).
Hidden Markov Models the HMMER programs developed by Sean Eddy. We use HMMs to dynamically generate alignments for our search interface.
CLUSTALX CLUSTALX is distributed as executables for DOS/Windows, Mac, and UNIX operating systems.
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.
Sequence Manipulation Suite contains an array of basic tools for manipulating DNA and protein sequences
READSEQ converts 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.
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.
Edinburgh University Molecular 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.
ClusterPicker at Edinburgh University, a tool for automatic identification of phylogenetic clusters.
PredictProtein 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.
Mullins Computational Biology Tools a suite of programs developed at the University of Washington 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.
ExPASy a large compilation of proteomics tools maintained by the Swiss Institute of Bioinformatics.
Viral Genomics Analysis Software a suite of tools at the Broad Institute for next-gen sequence assembly, primer design, etc.
SeqFeatR a tool to identify amino acids motifs and patterns in sequences.
HIV/AIDS Tools and Research Resources
HIVQ.PL performs command-line queries of the LANL HIV Sequence Database.
NCBI HIV Subtyping tool performs BLAST-based subtyping of an HIV-1 sequences.
REGA Viral Subtyping BioAfrica viral subtyping tool, which uses phylogenetic methods to identify HIV-1 subtype.
SCUEAL Subtyping DataMonkey tool that uses a network-based model to find HIV-1 subtype.
HIV Mutation Browser A database of mutagenesis and mutation information on HIV collated by computational text-mining.
Geno2Pheno (G2P) is a web based tool for prediction of coreceptor usage for HIV-1 based on V3 sequences. Please see: European guidelines on the clinical management of HIV-1 tropism testing
European guidelines on the clinical management of HIV-1 tropism testing
WebPSSM, a web based tool for prediction of R5/X4 phenotype based on V3 sequences.
Tools for recombination detection, a page maintained by Jun Fan and David Robertson.
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 drug resistance mutation 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
HIV BioAfrica presents the research, software and publications of Tulio de Oliveira, Sharon Cassol and members of their research groups
The HIV Brain Sequence Database HIV Sequences isolated from brain or other tissues from a subject where brain tissue was also sampled
AIDS Information at the National Institutes of Health (NIH), maintained by the National Institute of Allergy and Infectious Diseases (NIAID)
AIDScience the HIV prevention and vaccine research site of the American Association for the Advancement of Science
AIDS at Answers.com
CHAVI Center for HIV-AIDS Vaccine Immunology, a project of the National Institute of Allergy and Infectious Disease
UNAIDS the United Nations Global Programme on AIDS
IAVI the International AIDS Vaccine Initiative
AVAC AIDS Vaccine Advocacy Coalition
AIDScience Archive HIV prevention and vaccine research site of the AAAS
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
HIV Immunology Information
LANL Molecular Immunology Database: Tools & Links an array of tools and links related to the immunology of HIV
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