Evolutionary and epidemiological analysis of Roka HIV outbreak
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This directory contains data for HIV, HCV, and HBV. The datafiles were created via the following pipeline.

  1. Merge date information with genetic sequences, writing date information in fasta headers.
  2. Align sequences using mafft-linsi.
  3. Check alignments visually in Geneious.
  4. For maximum likelihood analyses convert .fasta to .phyx using seqmagick.