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LEA: an R package for Landscape and Ecological Association Studies

Bioconductor version: Release (3.19)

LEA is an R package dedicated to population genomics, landscape genomics and genotype-environment association tests. LEA can run analyses of population structure and genome-wide tests for local adaptation, and also performs imputation of missing genotypes. The package includes statistical methods for estimating ancestry coefficients from large genotypic matrices and for evaluating the number of ancestral populations (snmf). It performs statistical tests using latent factor mixed models for identifying genetic polymorphisms that exhibit association with environmental gradients or phenotypic traits (lfmm2). In addition, LEA computes values of genetic offset statistics based on new or predicted environments (, genetic.offset). LEA is mainly based on optimized programs that can scale with the dimensions of large data sets.

Author: Eric Frichot <eric.frichot at>, Olivier Francois <olivier.francois at>, Clement Gain <clement.gain at>

Maintainer: Olivier Francois <olivier.francois at>, Eric Frichot <eric.frichot at>

Citation (from within R, enter citation("LEA")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

LEA: An R Package for Landscape and Ecological Association Studies PDF R Script
Reference Manual PDF


biocViews Clustering, Regression, Software, Statistical Method
Version 3.16.0
In Bioconductor since BioC 3.1 (R-3.2) (9.5 years)
License GPL-3
Depends R (>= 3.3.0), methods, stats, utils, graphics
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Follow Installation instructions to use this package in your R session.

Source Package LEA_3.16.0.tar.gz
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macOS Binary (x86_64) LEA_3.16.0.tgz
macOS Binary (arm64) LEA_3.16.0.tgz
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