Welcome to PhyloD

HIV, like most retroviruses, is characterized by a tremendous rate of mutation, which leads to a high level of genetic diversity within and among patients. This genetic variation is the substrate for rapid within-host evolution. As our immune system learns to target the virus, the virus adapts, leading to an endless game of cat-and-mouse. From a scientific perspective, this provides a useful opportunity: if HIV is constantly adapting to our individual immune responses, then studying HIV adaptation will provide insights into both virus function and basic immunology. Over the years, Microsoft Research has developed models of viral adaptation that have allowed us to do just that. The tools we have developed for that purpose are provided as a service on this website. To download source code and executables, visit our download page.

Tools

  • HLA Completion: This tool will probabilistically "complete" missing or low-resolution HLA-I (loci A,B,C) typing data based on ethnicity. In the process, it will infer ethnicity if unknown.
  • Adaptation: Computes adaptation of HIV sequence to HLA-I alleles and to individual's HLA-I profiles. Will compute autologous, heterologous and circulating adaptation.
  • HLA Similarity: The transmission index of an HIV sequence estimates its relative fitness for transmission. This estimate is predominantly derived from the similarity of protein sequences to those circulating in the population.
  • Escape Mapping: Maps sites that are adapted and non-adapted for each sequence, given a set of escape associations.
  • Transmission Index: The transmission index of an HIV sequence estimates its relative fitness for transmission. This estimate is predominantly derived from the similarity of protein sequences to those circulating in the population.