Difference between revisions of "PhyloBayes"
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Moskalenko (talk | contribs) m (Text replace - "{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}" to "{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} ") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] |
| − | + | {|<!--Main settings - REQUIRED--> | |
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|{{#vardefine:app|phylobayes}} | |{{#vardefine:app|phylobayes}} | ||
|{{#vardefine:url|http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm}} | |{{#vardefine:url|http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm}} | ||
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|{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
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|{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | |{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | ||
|{{#vardefine:faq|}} <!--Enable FAQ section --> | |{{#vardefine:faq|}} <!--Enable FAQ section --> | ||
| − | |{{#vardefine:citation|}} <!--Enable Reference/Citation section --> | + | |{{#vardefine:citation|1}} <!--Enable Reference/Citation section --> |
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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. | 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. | ||
| − | <!-- | + | <!--Modules--> |
| − | + | ==Environment Modules== | |
| − | == | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
| − | + | ==System Variables== | |
| − | < | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
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* HPC_PHYLOBAYES_BIN - executable directory | * HPC_PHYLOBAYES_BIN - executable directory | ||
* HPC_PHYLOBAYES_DOC - documentation directory | * HPC_PHYLOBAYES_DOC - documentation directory | ||
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{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#if: {{#var: policy}}|==Usage Policy== |
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
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*'''Q:''' **'''A:'''|}} | *'''Q:''' **'''A:'''|}} | ||
{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
| − | If you publish research that uses {{ | + | If you publish research that uses {{#var: app}} you have to cite it as follows: |
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| + | 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. | ||
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| + | Lartillot N, Philippe H (2006) Computing Bayes factors using thermodynamic integration. Syst Biol 55: 195–207. | ||
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| + | 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. | ||
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Latest revision as of 20:20, 12 August 2022
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.
Environment Modules
Run module spider phylobayes to find out what environment modules are available for this application.
System Variables
- HPC_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.