SambaR: An R package for fast, easy and reproducible population‐genetic analyses of biallelic SNP data sets

Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels

(2020) Alina Thaden et al.   Molecular Ecology Resources

Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene

(2020) Menno J. Jong et al.   MOLECULAR ECOLOGY

BA3‐SNPs: Contemporary migration reconfigured in BayesAss for next‐generation sequence data

(2019) Steven M. Mussmann et al.   Methods in Ecology and Evolution

Fast inference of individual admixture coefficients using geographic data

(2018) Kevin Caye et al.   Annals of Applied Statistics

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Allele frequency-free inference of close familial relationships from genotypes or low depth sequencing data

(2018) Ryan K Waples et al.   MOLECULAR ECOLOGY

High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote (Canis latrans ) populations

(2018) Elizabeth Heppenheimer et al.   Ecology and Evolution

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

(2016) W. Chris Funk et al.   MOLECULAR ECOLOGY

pcadapt: anRpackage to perform genome scans for selection based on principal component analysis

(2016) Keurcien Luu et al.   Molecular Ecology Resources

Assessing polar bear (Ursus maritimus) population structure in the Hudson Bay region using SNPs

(2016) Michelle Viengkone et al.   Ecology and Evolution

Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model through Trimming the Distribution of FST

(2015) Michael C. Whitlock et al.   AMERICAN NATURALIST

hybridcheck: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data

(2015) Ben J. Ward et al.   Molecular Ecology Resources

Exploring population size changes using SNP frequency spectra

(2015) Xiaoming Liu et al.   NATURE GENETICS

LEA: AnRpackage for landscape and ecological association studies

(2015) Eric Frichot et al.   Methods in Ecology and Evolution

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

The Split-Apply-Combine Strategy for Data Analysis

(2015) Hadley Wickham   Journal of Statistical Software

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Confidence Intervals for Population Allele Frequencies: The General Case of Sampling from a Finite Diploid Population of Any Size

(2014) Tak Fung et al.   PLoS One

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

(2014) Zhian N. Kamvar et al.   PeerJ

StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations

(2013) Luke W. Pembleton et al.   Molecular Ecology Resources

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS