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Ecologie des Forêts Méditerranéennes

Unité de Recherches Ecologie des Forêts Méditerranéennes

ESEB 2015 MEETING

Poster supplementary information

Sampling and data production

Characteristics of the sampling sites and general outline of the methods used to obtain sequence data.
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Pipeline for the G2D test

Overview of the required steps for performing the “G2D” test (Nielsen et al. (2009) Genome Res. 19:838) on bidimensional site-frequency spectra.
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Estimation of parameters and simulation of population data

The scenario shown in the figure was used for both parameter estimation and simulations of 2D-SFS's conditional on the most-likely set of...
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Empirical G values

Check out the distribution of empirical (i.e; simulated) G values for the two pairs of populations.
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R script for computation of 2D-SFS from frequency tables

This script allows one to take population SNP variant frequency data and compute 2D-SFS for each pair of populations. All scripts are provided in...
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R script for computation of 2D-SFS from .arp files

This script allows one to take multiple-population SNP genotype data in the .arp (Arlequin) format and compute 2D-SFS for each pair of...
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R script for computation of G values

This script allows one to take a set of pairwise 2D-SFS and compute G values for individual contigs from one pair of populations. All scripts are...
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R script for computation of G values from multiple simulation files

This script embeds the functions fromArpToSFS() and G2DcalcMultipop() (see the corresponding files) and allows one compute G values from multiple...
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Utility for computing P-values

This script computes P-values for experimental G values, based on empirical distribution of P-values computed by multiG2DcalcMultipop(). All scripts...
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Utility to plot genome-level 2D-SFS

This script plots a shade-of-grey two-way plot where shade intensity represents the number of occurrences in each cell. All scripts are provided in...
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Utility to plot contig-level 2D-SFS

This script superposes the distribution of SNPs from given contigs to the genome-level distribution produced with gridPlot.txt All scripts are...
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Hierarchical Bayesian Modelling and Outlier detection (SNP level)

This method is original and described in a paper in preparation, and will not be further described here.
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