HIERFSTAT , a package for R to compute and test hierarchical F -statistics

By Jérôme Goudet. 2005

2,586 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/2e4647823e17f26358c884d60a84dd7d25a4b199

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Plant Science

Citations in the corpus

Genomic Selection in Plant Breeding: A Comparison of Models (2012, methodology): “The relevance of subpopulation structure was investigated with the pairwise F statistics quantifying the diff erences in allele frequency among subpopulations (Fst), estimated with a jackknifed estimator, as well as with a test of signifi cance of the subpopulation structure on the diff erentiation ”
Genetic differentiation and secondary contact zone in the seagrass Cymodocea nodosa across the Mediterranean–Atlantic transition region (2008, methodology): “In order to quantify the effect on genetic differentiation caused by the Atlantic–Mediterranean transition zone, we employed a hierarchical F-statistics analysis (hierfstat software, Goudet, 2005; Trouve et al., 2005).”
Maintaining tiger connectivity and minimizing extinction into the next century: Insights from landscape genetics and spatially-explicit simulations (2017, methodology): “We then calculated heterozygosity based differentiation statistics (PopGenReport 144 (Adamack & Gruber 2014), MMOD (Winter 2012), and HIERFSTAT (Goudet 2005) in R (Ihaka & 145 Gentleman 2012)).”
PopGenReport: simplifying basic population genetic analyses in R (2014, background): “RICHNESS function in the HIERFSTAT package (Goudet 2005) but is capable of working with genind objects and can handle polyploid organisms.”
Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars (2013, methodology): “The hierarchical F statistics, estimated from all SNPs as the ratio of sums of variance components (31), showed that the proportion of genetic differentiation explained by geographic location (13.”
adegenet: a R package for the multivariate analysis of genetic markers (2008, methodology): “Until now, data could only be imported into R from FSTAT (Goudet, 2002) using the hierfstat package (Goudet, 2005).”
Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality (2015, methodology): “Assessments of population structure through methods such as hierarchical F st (Goudet, 2005) and AMOVA (Michalakis and Excoﬃer, 1996 ) require hierarchical sampling of populations across space or time (Linde et al., 2002; Grünwald and Hoheisel, 2006; Everhart and Scherm, 2015).”
StAMPP: an R package for calculation of genetic differentiation and structure of mixed‐ploidy level populations (2013, methodology): “…on alternative software packages, such as adegenet (Jombart & Ah-med 2011), SPAGeDi (Hardy & Vekemans 2002), pegas (Paradis 2010), hierfstat (Goudet 2005), GenAlEx (Peakall & Smouse 2006) and Arlequin (Excofﬁer & Lischer 2010) as it implements genome relationship statistics and estimates…”
diveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors (2013, background): “2010), SMOGD (Crawford 2010), mmod (Winter 2012), hierfstat (Goudet 2004) or SPADE (Chao& Shen 2003).”