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This is RAxML version 8.2.9 on the CyVerse UK hardware (12 cpus, 256 GB per job). It is software to determine the best phylogenetic tree based on a sequence alignment using Maximum Likelihood (ML) statistical modeling. See http://sco.h-its.org/exelixis/web/software/raxml/index.html for more info.
- The only necessary parameters are the input file, algorithm and model, for which the defaults should be ok.
- Depending on your data, make sure to select the right model (Nucleotide, Protein, Binary).
- All parameters have their command line option mentioned, for easy searching in the manual
Use at least:
- An alignment file
The example files also show a DNA / protein combined example file with a pairing partitions file.
For explanation of the other possible files see the manual.
Depends on the action, but at least:
- RAxML.log - job log file
- RAxML.out - job output messages
- RAxML.err - job error messages
- RAxML_parsimonyTree.out - Starting tree used by RAxML
- RAxML_result.out - depending on the algorithm and options, the best phylogenetic tree found by RAxML
- RAxML_bestTree.out - the best phylogenetic tree found
- RAxML_info.out - RAxML specific output messages
- RAxML_log.out - RAxML general log
- RAxML_result.out - the result of your analysis (usually the same as the bestTree file)
Other files may appear depending on your model, partitions, options etc...
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