
LocalDiff (formerly Friction):
To characterize nonstationary patterns of isolation by
distance

Description 
Nonstationary 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

DuforetFrebourg
N, MGB Blum. Nonstationary patterns of isolationbydistance:
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, 30:513525 (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. Crossvalidation
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, 3:475479 (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 
Description 
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 webaccess 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, 22:363364 (2005)
