This is an important release of BayeScan, containing new features, bug corrections, and updated R scripts.

New features:

The command line version of BayeScan has been optimized to work on multicore processors. In practice this means that it will be much faster than previous versions as most machines now have at least 4 cores. This has been done using the very convinient OpenMP API for parallel programming. Unfortunatly, for the moment the Windows graphical version does not support this feature... We encourage people with large data sets to use the command line version which is also available under windows, and does support this feature!
BayeScan now directly calculates q-values for each locus and we encourage users to use (and report) this measure to make decisions. q-values are the False Discovery Rate (FDR) analogue of the p-value. The q-value of given locus is the minimum FDR at which this locus may become significant. In practice, if you choose, for example, a q-value threshold of 10%, it means that 10% of the corresponding outlier markers (those having a q-value lower than 10%) are expected to be false positives.

Improvements:

The MCMC trace output file (*.sel) no longer contains the alpha (selection) parameters by default, as it can lead to very large files when using a large number of markers. It is still possible to do it by using the -all_trace option in the command line.
The R plot script has been updated to directly use the q-values calculated by BayeScan. It is now much faster and plots the q-value on the x-axis instead of the PO. It also adds the option to highlight a particular set of makers.

BayeScan remained stuck when a codominant marker was declared in the input file to have a single allele (monomorphic marker).