BMC Enoplid Phylogeny Paper

Have been running jobs and annotating trees all day now that CIPRES is back up and running.

For the topological tests, decided only to run the “Long Branches and Outliers Removed” as one run, instead of doing both LBs and Outliers separately.  I don’t think these tests are that important compared to the outgroup tests but I wanted to run them anyways.  So, the following taxa were removed:

Outliers:

  • Desmoscolex spp.
  • Isolaimum sp.
  • Aulolaimus oxycephalus
  • Odontopharynx longicaudata
  • Myolaimus sp.

Long Branch Taxa:

  • Panagrolaimidae
  • Aphelenchoidea
  • Strongyloidoidea

Re-running jobs for BMC Enoplid Paper

I’ve been re-running all the jobs for the BMC paper, now including the Rhabdolaimidae for the Enoplid-only tree.  However, inclusion of these sequences has caused some (previously resolved) nodes to become unresolved.  So I’ve modified two new RAxML jobs to include 1000 bootstrap replicates and another with an extended majority rule consensus tree.  I’m also re-running the Enoplid Bayes tree to run for 4 million generations.

Did something similar with the Nematomorpha tree (Bayesian), using the nexus file for the thesis job Holly_longjob2 (CIPRES Bayes folder on old Dell).  Running this for 3 million and 4 million generations.

Productive Friday

Today I continued the edits on the BMC paper.  Left off at the start of the Discussion section.

Also commenced work on the Metagenomics Phylogenies.  Uploaded both the 95A and 95B OCTU sequences into CIPRES and am now running the Muscle alignments for those sequences.  Asked way to modify the 99A OCTU sequence names to include the corresponding 95A OCTU.

To do for Monday:

  • Send Fangning comments regarding the OCTU database
  • Put together the presentation for Steve Jones on Monday.

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.