Evolutionary and epidemiological analysis of Roka HIV outbreak


We did two principal analyses for HCV1b and HCV6e sequences. The HCV-1b alignment contains 39 sequences from Roka and 37 control sequences. The HCV-6e alignment contains 52 sequences from Roka and 20 control sequences. All sequences are partial portions of the NS5B gene.

  1. Maximum likelihood analysis for HCV6e and HCV1b
  2. Estimate temporally-resolved phylogenies for HCV1b and HCV6e to date outbreak clades