Getting started at UNH

Resurrecting my online lab book so that I remember what I do!

David Lunt sent back his comments regarding the (now combined) BMC papers detailing the Enoplid phylogeny.  He pointed out some of my outgroup choices, so I’ve had to go back and re-run a couple of the trees.

Just FYI in ARB, to export secondary structure features:

  • Helix, box reads  . 0 – =
  • Loops, box reads [<>]

I removed the Chromadorid outgroups and many Dorylaimid species from the Enoplid-only ML trees and ran the following jobs:

  • Raxml Job #891091  11Mar10_EnopReducedDS.phylip  (Normal ML run with Dorylaimia OGs)
  • Raxml Job #894968  DO NOT USE!  Forgot to add data partition file
  • Raxml Job #896361 11MarEnop_LSU_ML (Normal ML run with Dorylaimia OGs)
  • Raxml Job #898456 11MarEnop_StemLoopCombo, partition fie Raxml_SL_11Mar.txt (Stem/Loop ML run with Dorylaimia OGs)

CIPRES portal was rejecting my Bayesian runs, so will try again today.

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