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Amphora-2 (Guillaume Jospin, Aaron Darling, Morgan Langille, Dongying Wu, Thomas Sharpton, Katie Pollard, Jonathan Eisen)


  • AMPHORA-2 is a reworked version of AMPHORA to include newer tools and newer markers.
  • AMPHORA is an Automated Phylogenomic Inference Pipeline for bacterial sequences. From a given a set of protein sequences, it automatically identifies 31 phylogenetic marker genes. It then generates high-quality multiple sequence alignments for these genes and make tree-based phylotype assignments.


Generate markers

  • See/ask DY on how to put together sequences for 1 marker
  • Pick Representatives. Test the different methods, need to agree on 1.
    • Use the MCL approach
    • Use the PD approach
    • Use (a) consensus sequence(s) from HMMemit

Identify hits

Generate alignments

Build a tree