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:
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!