RAxML run

Ran the first RAxML run over the weekend (Job 418163).  ed of all of my own Enoplid Sequences (#256) and all the ‘Enoplid*’ search results by taxonomy in ARB, as well as Sabatieria sequences (6) chosen as the outgroup.  The file was subbmitted in Phylip format (filename Enoplids_2_28May.phy, total taxa=444)

  • GTR +G, ML estimate of alpha-parameter, 100 bootstrap replicates performed
  • Final ML Optimisation Likelihood  = -57408.599186
  • Annotated the best-scoring ML tree with bootstrap value

RAxML Job 418200 –>  Cox1_Ts_replaced.phy (this file has since been renamed ‘SSU_Ts_replaced.phy’).  Job was submitted on May 28th, and has not finished as of this morning. Estimated to take 145 hours.  URL: http://phylobench.vital-it.ch/raxml-bb/index.php?jid=418200

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Cox1 ML and Bayesian Treebuilding

 

Model choice for ML –> Use Modeltest 3.7 (chooses between 56 models)

  • Cox1_28May_aln.nex –> Cox1 Enoplids only with 6 Pellioditis spp. (105 taxa  total)

Ran on modeltest:

  1. First execute data file (Nexus) in PAUP
  2. Execute file ‘modelblock PAUP b10’ to compare models—this makes an output file called  ‘model.scores’ and you can change this filename afterward to reflect your data
  3. Deposit the ‘model.scores’ file into C:\bin folder and then run modeltest <inputfile.scores> outputfile.out
  4. If successful, the command line will revert back to C:\bin and the outfile is written to the bin folder.

For Cox1_28May_aln.nex the AIC selected GTR +I +G as the appropriate model for Cox1 data

 

Modeltest for MrBayes –> Use MrModelTest2.3 (chooses between 24 models)

  1. Execute data file (Nexus) in PAUP
  2. Execute ‘mrmodelblock’ in PAUP to compare models.  This makes an ooutput file called ‘mrmodel.scores’
  3. Deposit the ‘mrmodel.scores’ in the bin folder, and run the command mrmodel2  <inputfile.scores> outputfile.scores
  4. If successful, the command line will revert back to C:\bin and the outfile is written to the bin folder.

For Cox1_28May_aln.nex the AIC selected GTR +I +G as the appropriate model for Cox1 data

 

PhyML run 29 May

  • Used file ‘Cox1_29May.phy’ (sequential  file format, 105 taxa)
  • GTR + I +G model, estimated invariable sites, estimated gamma distribution, 4 nt substitution categories, base frequency estimate was empirical
  • Loglikelihood from stat file = -11260.10740

Running files in MrBayes:

  • Save as a sequential Nexus file (PAUP 4.0) from Mega
  • No need for alteration to MrBayes block—use the default one from the Barry Hall Book (chapter 8 folder).  For Cox1 I used the one with codon partitions.
  • Ran file ‘Cox1_28May_aln.nex’ using GTR +G+I with a codon partition model. Ran for 1,000,000 generations, final average standard deviation was 0.042370.
  • Burnin=1250 (should have increased this for 1,000,000 gen), sampplefreq=100 (records tree/parameters every 100 gen), printfreq=1000 (prints to screen every 1000 gen), nchains=4, temp=0.2

 

Bayes_datafile_changes