LFMM¶
Description¶
LFMM can be used for screening genomes for signatures of environmental adaptation in genomes (but it can be used for other types of GWAS). LFMM estimates confounders when identifying genetic polymorphisms that exhibit correlation with environmental gradients or other variables like phenotypic traits. The confounders - or latent factors - are then included in a statistical model for testing association between genotypes and the variable of interest. The original method implements latent factor mixed models based on a Bayesian bootstrap approach (C program LFMM 1.5 and R package LEA). The most recent implementation of LFMM is based on least squares estimates (R package lfmm). The "lfmm" R package
Environment Modules¶
Run module spider lfmm to find out what environment modules are available for this application.
Environment Variables¶
- HPC_LFMM_DIR - installation directory
- HPC_LFMM_BIN - executable directory
- HPC_LFMM_DOC - documentation directory
- HPC_LFMM_EXE - examples directory
Citation¶
If you publish research that uses lfmm you have to cite it as follows:
Categories¶
biology, phylogenetics