BCM - Computational and Mathematical Biology  


PCAdapt: To detect footprints of local adaptation using a Bayesian factor model
Description PCAdapt infers population structure and identify outlier loci that are candidates for local adaptation. PCAdapt is based on a hierarchical factor model where population structure is captured using K latent factors. In order to identify candidates for local adaptation, the hierarchical factor model searches for loci that are atypically related to population structure as measured by the latent factors.

How to cite

Luu K, E Bazin, MGB Blum. pcadapt: an R package to perform genome scans for selection based on principal component analysis. Molecular Ecology Resources 1:67-77 (2017)

LocalDiff (formerly Friction): To characterize non-stationary patterns of isolation by distance
Description Non-stationary patterns of isolation by distance arise when genetic differentiation between populations (or between individuals) increases at different rates in different regions of the habitat. Typical patterns include barriers to gene flows, secondary contact zone, corridors for gene flow, or gradients of gene flow across the species range. Using bayesian kriging, we provide estimates of local genetic differentiation across the species range. Typically measures of differentiation includes Fst and correlation measures.

How to cite

Duforet-Frebourg N, MGB Blum. Non-stationary patterns of isolation-by-distance: inferring measures of local genetic differentiation with Bayesian kriging. Evolution (2014)

R functions for anisotropic analyses: regression_method.R, geometric_method.R
Description These two functions provide the geographical directions of main genetic differentiation using a matrix of pairwise Fst values as input data. The function based on the regression method additionally provides a statistical test for anisotropy. The datafile data.txt provides an example of input data.

How to cite

Jay F, Sjödin P, AE Sjöstrand, M Jakobsson, MGB Blum. Anisotropic isolation by distance: the main orientations of human genetic differentiation. Molecular Biology and Evolution, 30:513-525 (2013)

abc:  Tools for Approximate Bayesian Computation (ABC)
Description abc is an R package that implements several ABC algorithms for performing parameter estimation and model selection. Cross-validation tools are also available for measuring the accuracy of ABC estimates, and to calculate the misclassification probabilities for the different models.

How to cite

 Csilléry K, O François, MGB Blum. abc: an R package for Approximate Bayesian Computation (ABC). Methods in Ecology and Evolution, 3:475-479 (2012)

POPS: Prediction Of Population Structure
Description The POPS program performs inference of ancestry distribution models. It computes individual cluster membership and admixture proportions based on multilocus genotype data and their correlation with environmental and geographical variables. Similarly to species distribution models, POPS provides routines to project cluster memberships and admixture proportions under scenarios of environmental change.

aPTreeshape is an R package dedicated to simulation and analysis of phylogenetic tree topologies using statistical indices. It is a companion library of the ape package. It provides additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access to public databases, and enables testing null models of macroevolution using corrected test statistics.

How to cite

N Bortolussi, E Durand, MGB. Blum and O Francois. APTreeshape: Statistical analysis of phylogenetic tree shape. Bioinformatics, 22:363-364 (2005)