Tree reconstruction exercise

• I have provided a subset of 100 simulated sequences of HIV in FASTA format from the PANGEA-HIV Methods Comparison Exercise, described here.
• These sequences have been generated from a known phylogenetic tree

• The sequences comprise of three HIV genes:

  • gag
  • pol
  • env

• Run neighbour joining and maximum likelihood analyses in order to reconstruct phylogenies

• Compare the topology of the tree to the true tree using the function treedist in the phangorn library