Computer programs for population genetics data analysis: a survival guide

By Laurent Excoffier, G. Heckel. Nature reviews genetics, 2006

389 citations recorded by the source corpus.

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Citations in the corpus

adegenet: a R package for the multivariate analysis of genetic markers (2008, methodology): “However, multivariate methods currently available in population genetics software are very restricted, despite the fairly large number of these programs (Excoffier and Heckel, 2006).”
LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method (2008, background): “Using fdist can be a challenging task for those not familiarized with command-line applications and requires a specific data format not used by other applications [9].”
diveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors (2013, background): “As a consequence of the growing suite of statistical genetics tools, which are often tailored to particular marker types, the analyses of population genetic data are becoming an increasingly complex task (Excoffier & Heckel 2006).”
Distribution modelling and statistical phylogeography: an integrative framework for generating and testing alternative biogeographical hypotheses (2007, neutral): “…those approaches that employ summary statistics (reviewed in Knowles, in press), as opposed to evaluating the full probability of the observed genetic data (reviewed in Excoffier & Heckel, 2006), because of the great flexibility and ease of computation that the summary-statistic approach offers.”
Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interface (2008, background): “Bayesian clustering algorithms have become extremely useful tools to investigate the structure of population genetics data (Excoffier and Henkel, 2006) but the conclusion drawn from the use of such algorithms can be markedly influenced by the presence of genotyping errors (Pompanon et al.”
pegas: an R package for population genetics with an integrated-modular approach (2010, background): “Currently, no uniﬁed framework for these programs exists making the use of the many different population genetics programs a complicated task (Excofﬁer and Heckel, 2006).”
PopGenReport: simplifying basic population genetic analyses in R (2014, background): “The large amount of data produced using microsatellite DNA markers have led to the development of a wide array of stand-alone statistical programs for the analysis of these data (e.g. Excoﬃer & Heckel 2006).”
What can DNA tell us about biological invasions? (2012, methodology): “…is highly structured in the native range (i.e., high levels of among-population variation), then genotypes found in introduced populations might be assigned with high probability to geographic locations within the native range using clustering or assignment methods (Excoffier and Heckel 2006).”
Restoring species through reintroductions: strategies for source population selection (2015, background): “The amount of within-population genetic variation is typically estimated using neutral markers and indices such as heterozygosity, allelic richness, or the proportion of polymorphic loci (for methods see Excoffier & Heckel 2006; Williams et al. 2014).”
Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0) (2010, methodology): “…(discrimination of scenarios and estimation of posterior distribution of parameters) were as followed: Uniform[1000; 20000] for and logUniform[2; 100] for the demographic parameters NS and NFi , respectively, and same distributions as those given in the text of Methods (section “ Mixing…”
Advances in molecular technology and their impact on fisheries genetics (2008, background): “New software packages for such analyses appear almost monthly and can make the choice of appropriate statistics difficult (Excoffier and Heckel 2006).”
Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study (2007, methodology): “Hence the power of geneland does not seem to rest on its ability to detect recent immigrants as claimed in (Guillot et al. 2005) and (Excoffier & Heckel 2006).”