BAPS 2: enhanced possibilities for the analysis of genetic population structure

By Jukka Corander, Patrik Waldmann, Pekka Marttinen, Mikko J. Sillanpää. Bioinform., 2004

476 citations recorded by the source corpus.

Subfields: Genetics, Statistics and Probability

View Paper: https://www.semanticscholar.org/paper/45cdbb81920f234169034545651fb41056d40ac1

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 Statistics and Probability

Citations in the corpus

INVITED REVIEW: What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity (2006, methodology): “We used structure as a representative of this type of analysis, but this is an active area of research and several other competing programs are available (e.g. Dawson & Belkhir 2001; Corander et al. 2004; Guillot et al. 2005).”
The worldwide expansion of the Argentine ant (2010, methodology): “…ant forms supercolonies that are highly genetically differentiated from each other, even when very closely located (Pedersen et al., 2006; Vogel et al., 2009), we used the Bayesian clustering method implemented in BAPS 4.14 (Corander et al., 2003, 2004) to assign nests to distinct genetic groups.”
Bayesian spatial modeling of genetic population structure (2008, methodology): “By incorporating the spatial information contained in y to the Bayesian predictive classification framework utilized in Corander et al. (2004), we can write the prior predictive distribution for the molecular data as p(x(N )|y) = ∑ S∈S p(x(N )|S)p(S|y).”
Clumpak: a program for identifying clustering modes and packaging population structure inferences across K (2015, methodology): “…population structure examines multilocus genotypes of individuals using model-based cluster analysis (Pritchard et al. 2000; Dawson & Belkhir 2001; Corander et al. 2003, 2004, 2008a,b; Falush et al. 2003, 2007; Guillot et al. 2005; Tang et al. 2005; Franc (cid:1) ois et al. 2006; Pella & Masuda…”
Effects of roads on patterns of genetic differentiation in red-backed salamanders, Plethodon cinereus (2008, methodology): “…and FST across the site for each locus To examine our data from another perspective, we used the program BAPS 4 (Bayesian Analysis of Population Structure; Corander et al. 2004; Corander and Marttinson 2006) to carry out further analyses of the effects of roads on genetic differentiation.”
Detecting loci under selection in a hierarchically structured population (2009, methodology): “Uncertainty about population structure We assume here that the genetic structure of the population is known in advance, but when this is not the case several approaches could be used to define this genetic structure from the data (for example, Pritchard et al., 2000; Dupanloup et al., 2002; Corander”
How race becomes biology: embodiment of social inequality. (2009, background): “In fact, the number of clusters necessary to describe global genetic variation has been inconsistent; some studies report five (Rosenberg et al., 2002) and others seven (Corander et al., 2004; Li et al., 2008).”
Repeatedly out of Beringia: Cassiope tetragona embraces the Arctic (2007, methodology): “However, these programs can also be used to infer latent groups based on dominant markers (Corander et al., 2004; Evanno et al., 2005).”
Genetic homogeneity in Juglans nigra (Juglandaceae) at nuclear microsatellites (2006, methodology): “We also applied a Bayesian approach to find the optimal partition of the 43 populations into groups consisting of populations with essentially identical allele frequencies, using the software BAPS (Bayesian Analysis of Population Structure, version 2; Corander et al., 2003, 2004).”
Introgression of crop alleles into wild or weedy populations (2013, methodology): “Recently, methods have been developed for assigning individuals into groups based on patterns of linkage equilibrium or genetic differentiation (e.g., Corander et al. 2004, Pritchard et al. 2000).”
Bayesian identification of admixture events using multilocus molecular markers (2006, background): “…sources contributing to data Under the assumptions stated in the Materials and Methods section, it is straightforward to extend the stochastic partition representing a genetic mixture in Corander et al. (2004, 2006) to a representation of a potentially admixed genetic composition of a sample.”
Phylogeny, phylogeography and genetic diversity of the Pisum genus (2010, methodology): “This has revolutionized phylogeny estimation by incorporating probability, the provision for measure of support and, especially, complex model and data character processing (Huelsenbeck et al., 2001; Holder and Lewis, 2003; Beaumont and Rannala, 2004; Corander et al., 2004).”
Integrating genetic data into management of marine resources: how can we do it better? (2008, background): “In the current decade, much more powerful and much more general genetic clustering programmes have been developed (Pritchard et al. 2000; Corander et al. 2004; Pella and Masuda 2006) which do not require any baseline data at all.”
Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation (2006, methodology): “Three of the most widely used software programs available for Bayesian clustering are PARTITION (Dawson and Belkhir 2001), STRUCTURE (Pritchard et al. 2000; Falush et al. 2003; Pritchard and Wen 2003), and BAPS ( Corander et al. 2003, 2004, 2005 ).”