Tools:

   1.  jpHMM (jumping profile Hidden Markov Model) tool for the detection of genomic recombinations in HIV-1
   2.  HIV BLAST
   3.  RIP (Recombinant Identification Program)
   4.  FindModel (analyzes alignment sequences to see which phylogenetic model best describes your data)
   5.  PhyML interface (fast and accurate heuristic for estimating maximum likelihood phylogenies)
   6.  NCBI HIV-1 Subtyping tool
   7.  Genotype-Treatment Correlations
   8.  Genotype-Phenotype Correlations
   9.  Genotype-Clinical Outcome Correlations
 10.  HIV Drug Resistance Summaries
 11.  Syn-SCAN (synonymous and nonsynonmous mutation rates calculation)
 12.  HIV nucleotide and protein alignments 
 13.  Subtype Reference Alignments 
 14.  Compendium Alignments 
 15.  Analysis & Detection of APOBEC-induced Hypermutation
 16.  HIV-1 Sequence Quality Control (QC)
 17.  SNAP (Synonymous Non-synonymous Analysis Program)
 18.  VESPA (Viral Epidemiology Signature Pattern Analysis)
 19.  Gene Cutter (Sequence Alignment and Protein Extraction)
 20.  HIV Sequence Locator
 21.  Format Converter (converts the sequence(s) to a different user-specified format)
 22.  SeqPublish (Sequence Alignment Publishing Tool)
 23.  HIV Treatment Websites
 24.  WHO(HIV-AIDS)
 25.  NIH AIDS Research and Reference Reagent Program
 26.  MEGA (a versatile, user-friendly program that does phylogenetic analysis and bootstrapping)
 27.  BioEdit (is a full-featured alignment editor for nucleotides and amino acids comes with built-in alignment and tree-building programs.)
 28.  Clustal: Multiple Sequence Alignment
 29.  Sequin (tools for sequence submission to GenBank (NCBI))
 30.  RECall (beta v2.10) - Web based sequence analysis
 31.  DataMonkey
 32.  Beast (Bayesian Evolutionary Analysis Sampling Trees)
 33.  REGA HIV Subtyping Tool  
 34.  Geno2Pheno
 35.  NIH AIDS Reagent Program
 30.  The HIV Brain Sequence Database
Developed by - NATH IT SOLUTION'S