Difference between revisions of "Bayenv"

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m (Maxprok moved page BAYENV to Bayenv: Fixed the name)
 
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<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
 
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
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* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
* HPC_{{#uppercase:{{#var:app}}}}_DOC - documentation directory
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* HPC_{{uc:{{#var:app}}}}_DOC - documentation directory
* HPC_{{#uppercase:{{#var:app}}}}_EXE - example directory
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* HPC_{{uc:{{#var:app}}}}_EXE - example directory
  
 
<!--Configuration-->
 
<!--Configuration-->

Latest revision as of 19:03, 10 June 2022

Description

bayenv website  

Loci involved in local adaptation can potentially be identified by an unusual correlation between allele frequencies and important ecological variables, or by extreme allele frequency differences between geographic regions. However, such comparisons are complicated by differences in sample sizes and the neutral correlation of allele frequencies across populations due to shared history and gene flow. To overcome these difficulties, we have developed a Bayesian method that estimates the empirical pattern of covariance in allele frequencies between populations from a set of markers, and then uses this as a null model for a test at individual SNPs. Graham developed this method in collaboration with David Witonsky, Anna Di Rienzo and Jonathan Pritchard.

Environment Modules

Run module spider bayenv to find out what environment modules are available for this application.

System Variables

  • HPC_BAYENV_DIR - installation directory
  • HPC_BAYENV_BIN - executable directory
  • HPC_BAYENV_DOC - documentation directory
  • HPC_BAYENV_EXE - example directory




Citation

If you publish research that uses bayenv you have to cite it as follows:

Coop G., Witonsky D., Di Rienzo A., Pritchard J.K. Using Environmental Correlations to Identify Loci Underlying Local Adaptation. Genetics. 2010