More SSU edits

The following groups were edited on May 27/28th:

  • Pellioditis
  • Meloidogyne
  • Neochromadora
  • Trochodorus

The following species look dodgy, and were labelled with ‘sourhope removed’ in the import field before being removed fromm the tree:

  • MlgInc34
  • MlgInc13
  • MlgInc21
  • MlgInc12
  • MlgHap10
  • MlgInc31
  • MlgInc20
  • MlgInc33
  • Sgd Vene2
  • SgdSter6
  • BrgMal14
  • BrgMala9
  • P25Paci5
  • Cb3Rema3
  • P25Paci4
  • UncRhab2
  • UncNem74
  • UncNem68
  • UnnN1414

The following sequences looked like they could be included in the final tree, but they need to be re-aligned using the PT server when that is set up.  They were removed for the time being, labelled with PT search (in the import field I think):

  • S94Batur (Soboliphyme)
  • Eu6Dispa (Eucoleus)
  • M65Tenui (Capillaria)

Today I also ran four trees on the RaxML web server.  I realised (after the fact) that two datasets were incomplete, so the correct job numbers:  Job _____, from the file ‘Enoplids_2_May28’ (Enoplid only tree, with Sabatieria as the outgroup) and Job 416526, from the file ‘Cox1_Ts_replaced’.

Continuing SSU edits

41 more nematodes were removed from the tree.  These included 38 unidientified Sourhope nematodes (labeled before removal), and 3 Canorhabditis specimens: Cb3Rema2, Cb3Bren2, Cb3Reman.  These last 3 specimens had awfully messy alignments that couldn’t be fixed by fast aligner.  The info field revealed that these sequences were resulting from a whole genome shotgun project, and so I suspect they are of dubious quality (or aren’t actually 18S sequences).  Pristonchus sequence P25Paci5 also looks dodgy but I left it in the tree for now.

The following groups were edited on May 25/26:

  • Caenorhabditis
  • Oscheius
  • Sphaerolaimus
  • Terschellingia
  • Prismatolaimus
  • Acrobeloides
  • Diplolaimelloides
  • Pristionchus
  • Spirinia/Robbea/Laxus (neighbours in a group)
  • Toxocara
  • Philonema
  • Plectus
  • Pikilolaimus
  • Anguillicola
  • Anoplostoma
  • Rotylenchus/Rotylenchulus
  • Diphtherophora
  • Campydora
  • Eucephalobus
  • Mesocriconema
  • Eudorylaimus
  • Naccobus

Cleanup of SSU tree in ARB

Today I started by cleaning up the tree a bit.  The Sourhope samples mostly didn’t add any information and just clogged up the tree, so I removed a total of 1922 unidentified Sourhope sequences from the tree–they are accessible in the ARB database, however..  They were marked with ‘sourhope removed’ in the import field.

The following groups were edited today:

  • Mesomermis
  • Monoposthia
  • Xiphinema
  • Pratylenchus
  • Phasmarhabditis
  • Strongyloides–the outlier sequences are a mess, although the main group is fine.  I removed species named ‘SgdRatt5’ and ‘RtdSpeci’ because they looked to be of bad quality.  They didn’t align coherently with fastaligner, and the sequences didn’t agree even the super-conserved regions.

I re-built the NJ tree at 9pm after today’s major edits–hopefully the groups will start falling into place.