RealSFS

This program will estimate the SFS based on a .sfs file generated from the ./angsd [options] -doRealSFS .

Brief overview

./emOptim2 afile.sfs nChr [-start FNAME -P nThreads -tole tole -maxIter  -nSites ]
nChr is the number of chromosomes. (twice the number of diploid invididuals)

Program defaults to use the EM algorithm for the optimisation, the BFGS method can used by supplying BFGS as the first argument after ./emOptim2

Output

Main results are printed to the stdout. Values are in logspace.

NB

Use as many sites as possible, for more reliable estimates.