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