Phylohackathon 1/BioPerl Targets

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  1. reconcile tree problem:
    msa + species_tree (e.g., bio::DB::Taxonomy -> njtree/phyml (or RAP) -> tree::NHX
    BioPerl already has alignment IO, tree IO
    1. wrapper around njtree
    2. wrapper around RAP
    3. naming issue (e.g., PHYLIP, clustalw) - assign short names, run external analysis, replace long names
  2. seq family analysis pipeline [Jason]
    blast (m9) -> tribemcl -> clustalw -> phylip -> paml
    1. mcl wrapper (fam_id, gene_name)
  3. phylogenetic footprinting (shadowing) [Sendu]
    PhastCons, FootPrinter, or use HyPhy?
    need to investigate the use of this software
    1. support input and output formats
  4. morpho characters: infer tree and support characters
    Rutger - CDAT, alignI
  5. estimate divergence times
    r8s, thornian time traveler, beast - need to generalize on input constraints and output
    Jason (or other) find out in/out formats
    1. generic interface to time estimate
  6. NEXUS serialization format