Cipres Web Portal

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RAxMLHPC

RAxML (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic trees. The program is explicitly being developed to efficiently infer trees for extremely large datasets, either in terms of the number of taxa and/or the sequence length. For example, a 25,000-taxon alignment of protobacteria with an alignment length of 1,500 base pairs had a run time on a single CPU of the cluster of only 13.5 days, with a memory consumption of only 1.5GB. Much additional information can be found on Alexis' RAxML page.

Through OpenMP-based parallelization of RAxML, the program can also efficiently exploit the SMP (Symmetric Multi Processing) capabilities of the cluster with its 8-way SMP nodes. This type of parallelism is especially useful for very long alignments. For example, together with Olaf Bininda-Emonds and Usman Roshan, we are currently working on a multi-gene analysis of almost 70 genes for a total of 2,100 mammal species.

Recently, rapid bootstrap heuristics for RAxML were released that are more than an order of magnitude faster than current algorithms. Computational experiments on 22 DNA and AA (amino acid) containing 125 up to 7764 sequences; the RBS inferences are between 8 and 20 times faster (average 14.73) than SBS analyses with RAxML and between 18 and 495 times faster than BS analyses with competing programs, such as PHYML or GARLI The performance improvement increases with alignment size. These are available through the CIPRES portals V 1.13 and V 2.0.

RAxML 7.0.4 is running on Cipres Portal V 1.13 and V 2.0.

A manual for RAxML is available. [pdf]

RAxML home page here.

INPUT = dna, protein, or mixed matrices in relaxed Phylip format.

Test input file (nucleic acid): raxml_input.phy

Optional Input: Partition File: a text file in the following format:
DNA, gene1=1-921
DNA, gene2=922-4015
(Note that "DNA" must be in all caps).

Test output file1 (run summary): RAxML_info_result.txt

Test output file2 (bootstrap result): RAxML_bootstrap_result.txt

Test output file3 (besttree): raxml_outtree.tre

If you use RAXML, please cite:

• Alexandros Stamatakis: ``RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models”. In Bioinformatics 22(21):2688-2690, 2006. (pdf)
• A. Stamatakis, P. Hoover, J. Rougemont. (2008) A Fast Bootstrapping Algorithm for the RAxML Web-Servers, Systematic Biology 57(5): 758-771.

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