Big Updates

Been doing a lot of updates over the past week or so. 

There are now separate ARB databases for the Enoplid-only tree (12June_EnopTree.arb)and the Full nematode tree (14June_FullNemTree.arb).     Firstly, I severely cut down the Full Nem SSU tree to 1798 taxa, and further to 1796 taxa on June 18thThe Enoplids-only tree now contains 784 taxa.

On the 12th June I edited the following genera in the Full Nem tree, during the process of cutting down taxa:

  • Oscheius
  • Phasmarhabditis
  • Plectus
  • Ancylstoma
  • Protorhabditis
  • Mesorhabditis
  • Schistonchus
  • Aphelenchoides
  • Camallus/Procamallus/Spirocamallus
  • Brugia
  • Toxocara
  • Philonema
  • Poikilolaimus
  • Howardula
  • Pratylenchus
  • Hirschmanniella
  • Basiria
  • Helicotylenchus
  • Cephalob*
  • Zeldia
  • Philometra/Philometroides
  • Nacobbus
  • Eumonhystera
  • Oxydirus
  • Labronema
  • Clavicaudoides
  • Robbea
  • Laxus
  • Caenorhabditis
  • Rhabditis
  • Panagrolaimus
  • Anguina
  • Aphelenchus
  • Adoncholaimus
  • Daptonema
  • Theristus

The Enoplids Only tree contains the following species:

  1. All Enoplea (I searched in tax_embl field for ‘Enoplea’ and selected all results)–includes Enoplida, Dorylaimia, etc.
  2. Chromadoridae (searched in tax_embl field for ‘Chromadoridae’)–represents outgroup
  3. Holly Enoplids (All sequences–no duplicates removed)

The total of the above Enoplids was 989 taxa.  This was then cut down to 784 by removing excess sequences in some taxa (but none of Holly Enoplids were removed) Some of the removed taxa are listed in the file 12June_removedEnop.alpha, but more were removed that aren’t listed in that file.

The alignment was checked for ALL Enoplid sequences by systematically going down the tree.  On June 13th (after all edits were finished), all Enoplid taxa left in tree (784 taxa) were submitted to RaxML:

  • Job 533582 –> 13June_EnopFulledit, GTR + G
  • Job 533583 –> 13June_EnopFulledit, GTR +G +I

On June 14th, the same Enoplid taxa were submitted for Bayesian Inference analysis via the CIPRES web server.  The taxa need to be exported from ARB in PAUP format, and then you need to add a) MrBayes command block b) Remove some info from the header (change RNA to DNA, delete some characters for missing data):

  • File 14_June_EnopBayes.nxs, GTR + G
  • File 14_June_EnopBayes.nxs, GTR + G +I

The next few days have been spent editing ALL taxa alignments in the Full Nem SSU tree.  These edits were finished on June 18th, and the Full Nem tree (no outgroups added yet) was submitted to RAxML:

  • Job 569141 –> 18June_FullNem.phy, GTR + G
  • Job 569160 –> 18June_FullNem.phy, GTR + G + I

I tried submitting the Full Nem tree to the CIPRES server for MrBayes, but it appears the file size is too big for the server to accept–I have to contact the administrators if I want them to run the job.