BCM - Computational and Mathematical Biology
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| Software |
| R functions for anisotropic
analyses: regression_method.R,
geometric_method.R |
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| 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. |
| abc:
Tools for Approximate Bayesian Computation (ABC) |
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| 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 of different models. |
| If you use the R package abc, please cite |
Csilléry K., O. François, M.G.B Blum. abc: an R package
for Approximate Bayesian Computation (ABC). Methods
in Ecology and Evolution, in press (2012) |
| POPS:
Prediction Of Population Structure |
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| 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 web-access to public databases, and
enables testing null models of macroevolution using
corrected test statistics.
|
| If you use APTreeshape, please cite | N. Bortolussi, E. Durand, M.G.B.
Blum and O. Francois. APTreeshape: Statistical analysis of
phylogenetic tree shape. Bioinformatics,
22:363-364 (2005) |
| Estimation of the number of ancestral lineages | |
| Description | A C++ code for estimating the number of ancestral lineages is provided. The code provides a coalescent simulator when the number of ancestral lineages at a fixed point of time has been fixed. The code is provided with absolutely no warranty. |
| If you use this program, please cite | M.G.B. Blum and N.A. Rosenberg. Estimating the number of ancestral lineages using a maximum likelihood method based on rejection sampling. Genetics 176: 1741-1747 (2007) |