User:R. Eric Collins/MBL/Rokas

Antonis Rokas

Evolutionary Genomics

• Kahn 2011 increase in sequencing quality over time
• CRAP: Cluster Reconstruction ... Phylogeny
  • find HGT of GAL cluster from Candida
  • Slot and Rokas 2010 PNAS

• sarcosine oxidase
  • gene trees --> species trees
  • map environmental sequences to tree (iTOL) in a heatmap, colors = environment type/source

• OASES seems to be the most popular for assembly
• Di-Align (?) local alignment a la pplacer

• Hittinger et al. 2010: using transcriptome to reconstruct species phylogenies
  • they needed 0.5--2 million 35bp reads from each species to get resolved phylogeny
  • reads assembled with velvet
  • contigs > 100bp, >300bp kept
  • identify RBBH "orthologs" __against outgroup__
  • keep loci with >1-4 species
  • locally align each cluster
  • concatenate
  • these will tend to be the most highly expressed regions
  • at $100/Gb this is coming to $10-50 per species