Question: RAxML bootstrap support output
0
gravatar for marcela.yoc
4.0 years ago by
marcela.yoc0 wrote:

Hi everyone!
I need your help to undestand the output files from EPA-RAxML analysis. I did the analysis, but the final tree do not have the bootstrap support. I would like to know which is the file that contain the bootstrap values or whether I should read the output files in another program.

 I got these output files:
 

Downloads

  • RAxML_labelledTree
  • RAxML_classificationLikelihoodWeights
  • RAxML_classification
  • RAxML_info
  • RAxML_portableTree.jplace
  • RAxML_originalLabelledTree
  • RAxML_entropy
  • alignment_file.sto
  • alignment_file2.sto
  • alignment_file.hmm
  • alignment_file
  • queryfile
  • treefile.phyloxml
  • treefile_no_placements.phyloxml
  • input_tree


Labelled reference tree including branch labels and query sequences written to file: /webdata/RAxMLWS/public/jobs/123xx/RAxML_labelledTree.124xx
Labelled reference tree with branch labels (without query sequences) written to file: /webdata/RAxMLWS/public/jobs/123xx/RAxML_originalLabelledTree.123xx
Labelled reference tree with branch labels in portable pplacer/EPA format (without query sequences) written to file: /webdata/RAxMLWS/public/jobs/123xx/RAxML_portableTree.123xx.jplace
Classification result file written to file: /webdata/RAxMLWS/public/jobs/123xx/RAxML_classification.123xx
Classification result file using likelihood wieghts written to file: /webdata/RAxMLWS/public/jobs/123xx/RAxML_classificationLikelihoodWeights.123xx
Classification entropy result file using likelihood wieghts written to file: /webdata/RAxMLWS/public/jobs/123xx/RAxML_entropy.123xx


I opened the file RAxML_labelledTree in Archaeopteryx, but  I did not get bootstrap value as confident value for branches.
I used as input file an alignment with bootstrap value in nwk format.

I also opened the file treefile.phyloxml which has a branch labels that I don't recognize.

Thanks in advance!
Marcela

job alignment • 2.6k views
ADD COMMENTlink modified 4.0 years ago by h.mon26k • written 4.0 years ago by marcela.yoc0

What was the command you used to run raxml? how many bootstraps did you run? did you ask to print the best ML tree? From the files it looks like it either didn't complete or you didn't run will all the options.

EDIT: specifically:

-N 1000 (to specify number of bootstraps)
-f a (to return the best ML tree with support values)
ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by arnstrm1.7k
0
gravatar for h.mon
4.0 years ago by
h.mon26k
Brazil
h.mon26k wrote:

Looking at the RAxML_info file I do not see the command-line options to perform bootstrap, which are either -b or -x. Did you run locally on the command-line, with a GUI, or on a server?

Besides, cross-posting is not good etiquette.

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by h.mon26k

@h.mon, we have lots of things in common, LOL!

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by arnstrm1.7k
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