new to fastsimcoal

[geek_y]

Hi All,

I am a bioinformatician and i am new to population genetic studies. I would like to know how do I make use of fastsimcoal ? I can run the examples given in the web-site and I get the output in arlequine project file. what should I do next with the fastsimcoal output ? How do I interpret the results of simulation and make sense of it ? I need some good starting material to read and understand these concepts.

[Ivan Scotti]

Hi,

if I get it right, your question is quite vast and does not seem to be exactly about the software package in itself, but rather about making yourself a background in population genetics... so, back to "square one", I'd say.
If I may suggest you a path, you may start by reading a population genetics textbook (e.g. P. Hedrick's "Genetics of populations"), then read literature about the coalescent (because this is what the business is about in fastsimcoal: applying the coalescent to infer population-genetic processes; you may start by reading the relevant chapters in Balding, Bishop, Cannings "Handbook of statistical genetics"), and then move to reading (at least) Arlequin's manual, which is in itself a course in population genetics... it will take time, but this way you'll know what you are doing with fastsimcoal, and why.

All the best,

Ivan

[Laurent Excoffier]

Thanks to Ivan Scotti for his advice to geek_y.

I fully agree with it.

In addition, I would also advise to read the fastsimcoal2 user manual, as well as our fastsimcoal2 paper in PLOS Genetics, which is fully refereced in the manual. This will be especially useful if you want to go beyond simulate patterns of diversity and estimate demographic parameters from genomic data.

Best

laurent