Difference between revisions of "PhyloBayes"
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===Serial=== | ===Serial=== | ||
*{{#var:app}} | *{{#var:app}} | ||
| + | ===Parallel (MPI)=== | ||
| + | *intel/2012 | ||
| + | *openmpi/1.6 | ||
| + | *phylobayes/1.4f | ||
| + | |||
==System Variables== | ==System Variables== | ||
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
Revision as of 02:12, 20 August 2013
Description
PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. Compared to other phylogenetic MCMC samplers, the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT (Lartillot and Philippe, 2004). CAT is a mixture model especially devised to account for site-specific features of protein evolution. It is particularly well suited for large multigene alignments, such as those used in phylogenomics.
Required Modules
Serial
- phylobayes
Parallel (MPI)
- intel/2012
- openmpi/1.6
- phylobayes/1.4f
System Variables
- HPC_{{#uppercase:phylobayes}}_DIR - installation directory
- HPC_PHYLOBAYES_BIN - executable directory
- HPC_PHYLOBAYES_DOC - documentation directory
Citation
If you publish research that uses phylobayes you have to cite it as follows:
Lartillot N, Phillipe H (2004) A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 21: 1095–1109.
Lartillot N, Philippe H (2006) Computing Bayes factors using thermodynamic integration. Syst Biol 55: 195–207.
Lartillot N, Brinkmann H, Philippe H. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol. 2007;7(Suppl 1):S4. doi: 10.1186/1471-2148-7-S1-S4.