RAxML bootstrap support output

Question

[marcela.yoc]

Hi everyone!

I need your help to understand 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

[arnstrm]

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)

Answer 1

[h.mon]

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.

[arnstrm]

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