Parallel calculation in dadi

[吴琦]

I want to work a very large data set with dadi which may include several million SNPs. It will be two slow for any single CPU to work. So I wonder whether dadi can perform multi processes mission. Therefore the calculation speed could be increased. I note that there is a RunInParallel.py script file in dadi package, but it seems it is not fully tested and not mentioned in manual file.

WQ

[Ryan Gutenkunst]

Hello WQ,

First, the computational speed of dadi depends on the number of
populations and the number of samples from each population. The total
number of SNPs doesn't matter. So several million SNPs is no problem.

Second, right now dadi is not really parallelized. Some aspects of the
optimization could be, if that becomes a bottleneck for you. I suggest
you try your problem first, to see whether heavy parallelization will
be worthwhile.

Best,
Ryan

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Ryan Gutenkunst
Assistant Professor
Molecular and Cellular Biology
University of Arizona
phone: (520)626-0569
http://gutengroup.mcb.arizona.edu