raxml-starttree-8.2.11 is an Agave app for using RAxML to to generate a random stepwise addition parsimony tree or completely randomized tree for use with ExaML or RAxML. You can choose a more superficial randomized stepwise addition parsimony tree (-X), a standard randomized stepwise addition parsimony tree (-y), or a completely random start tree (-d).
The raxml-starttree-8.2.11 app runs on the Stampede2 supercomputer at the Texas Advanced Computing center. It uses an executable from the RAxML repo, version 8.2.11, built using Makefile.AVX2.gcc. The maximum run time is two hours, but this should be enough to generate a start tree for most input alignments.
Please cite the following paper when using raxml-RFdistance-8.2.11 and RAxML:
A. Stamatakis: "RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies". In Bioinformatics, 2014, open access.
raxml-starttree-8.2.11 requires an input alignment file in relaxed PHYLIP or FASTA format. A partition model is not required.
For additional information on this tool, please consult the RAxML manual.
Use the alignment file
as test data. It can be accessed by navigating to:
When the app is run in the Discovery Environment, use the following parameters with the above input file to get the output provided in the next section below.