RAxML is a hybrid code created by a collaboration between Alexandros Stamatakis and Wayne Pfeiffer. The Portal provides a familiar Black Box interface (at phylobench.vital-it.ch) and an advanced interface. This interface submits to a large NSF XSEDE Resource. These machines allow your job to run for up to 168 hours (7 days). RAxML on CIPRES ONLY accepts matrices in relaxed Phylip format.
How to use it: Submission to XSEDE requires the user to provide parameters that determine job priority in the queue, help identify the number of processors required, and set a time for job termination (whether the run is finished or not). First time users should view the primer on using XSEDE resources here. With either interface, most of decisions are made automatically, based on settings the user selects (advanced interface) or pre-set values (Black Box interface). However, both interfaces require the user to enter the number of characters in the the matrix. The value you enter can be approximate, just make sure it is pretty close.
Disadvantages:The queue times on XSEDE resources vary according to traffic and according to the size of your job (shorter jobs typically have shorter queue waits). Sometimes XSEDE resources go down for preventative maintenance or due to unforeseen circumstances. At present, this will cause your job to fail, and you will have to restart it. There is no restart capability at present.
The RAxML Google Group is here.
The RAxML Manual is here.
If you use RAxML, please cite:
Stamatakis, A. (2014) RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Bioinformatics 10.1093/bioinformatics/btu033 http://bioinformatics.oxfordjournals.org/content/early/2014/01/21/bioinformatics.btu033.abstract
If there is a tool or a feature you need, let us know.
CIPRES – Cyberinfrastructure for Phylogenic Research