Phylohackathon 1/BioPerl Targets

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