Difference between revisions of "LFMM"

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[[Category:Software]][[Category:Biology]][[Category:Genomics]]
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[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
 
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{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|lfmm}}
 
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<!--Modules-->
 
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==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_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory

Latest revision as of 19:50, 15 August 2022

Description

lfmm website  

The LFMM computer program includes an integrated framework based on population genetics, ecological modeling and statistical techniques for screening genomes for signatures of local adaptation.

It implements fast algorithms using latent factor mixed models based on a variant of Bayesian principal component analysis in which residual population structure is introduced via unobserved factors.

Environment Modules

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

System Variables

  • HPC_LFMM_DIR - installation directory
  • HPC_LFMM_BIN - executalbe directory
  • HPC_LFMM_EXE - example directory




Citation

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

E. Frichot, S.D. Schoville, G. Bouchard, O. François Testing for associations between loci and environmental gradients using latent factor mixed models Molecular Biology and Evolution, in press 2013. Link to MBE.