Sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. #Phylogenetic tree inference #DNA alignment inference #AA alignment manipulation #Phylogenetic tree #DNA alignment #Inference
RAxML (Randomized Axelerated Maximum Likelihood) is a free and open source, command line based tool for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees.
RAxML has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package. In addition to the sequential version, RAxML offers two ways to exploit parallelism: fine-grained parallelism that can be exploited on shared memory machines or multi-core architectures and coarse-grained paral- lelism that can be exploited on Linux clusters. The current version of RAxML is a highly optimized program, which handles binary, DNA, RNA secondary structure, multi-state morphological, and AA alignments under various models of substitution and several distinct methods of rate heterogeneity.
How to install and run: Unarchive, open a Terminal window, go to the RAxML's folder and run the following commands from the command line:
make -f Makefile.gcc ./raxmlHPC
To have RAxML run about 30-50% faster:
make -f Makefile.SSE.gcc ./raxmlHPC-SSE3
One may also compile a Pthreads version with and without SSE3 intrinsics:
make -f Makefile.PTHREADS.gcc ./raxmlHPC-PTHREADS
and for a 30-50% performance boost: make -f Makefile.SSE3.PTHREADS.gcc ./raxmlHPC-PTHREADS
What's new in RAxML 7.2.8 Alpha:
- several bug fixes
- added some new protein substitution models: MTART, MTZOA, PMB, HIVB, HIVW, JTTDCMUT, FLU
RAxML 7.2.8 Alpha
add to watchlist add to download basket send us an update REPORT- runs on:
- Mac OS X (-)
- file size:
- 236 KB
- main category:
- Math/Scientific
- developer:
- visit homepage
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