Include Page | ||||
---|---|---|---|---|
|
This Application has been archived. Please see the new RAxML 8.1.17 app.
...
App Name
RAxML implements a rapid maximum likelihood-based inference of large phylogenetic trees from nucleotide multiple sequence alignments.
Quick Start
- To use RAxML, upload your data in relaxed PHYLIP format (sequential or interleaved, no name length restrictions).
- Resources: documentation
Test Data
All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:
Community Data > iplantcollaborative > example_data > raxml_nucleotides
Input File(s)
Use campanulaceae.phy.reduced as test data.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Default parameters only.
- You must select a model. GTRCAT works.
Output File(s)
Expect as output:
- RAxML_bestTree.tree.nwk: best Rapid ML tree
- RAxML_info.tree.nwk: run info
- RAxML_log.tree.nwk: run log
- RAxML_parsimonyTree.tree.nwk: parsimony-generated base tree
- RAxML_result.tree.nwk: result tree
Please note that due to the randomization of the algorithm, your outputs may not be EXACTLY the same as those listed in the example data directory.
Tool Source
...