Fwd: SNPs input file for Nemo

[Frederic Guillaume]

Hi Frederic,


My name is Iván Vera and I am a postdoc at Universidad Católica de la
Santísima Concepcón in Chile. I have worked with Nemo before and have
published a few articles simulating different scenarios in frehwater
fihes using microsatellite markers. Right now I am working with SNPs
from crabs and some algae and I am planning to use Nemo again for some
simulations using my own SNPs sequences for the source population. I was
wondering if you have an exmaple of a SNPs input file I could use to get
familiar with it to run some simulations on Nemo?


Regards,


*Dr. Iván Vera Escalona*

https://www.researchgate.net/profile/Ivan_Vera-Escalona
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[Frederic Guillaume]

Hi Ivan,

You can import SNP data the same way as you'd import microsatellite data with an FSTAT file. In the FSTAT file, you have to code the alleles (di-allelic) as '1' and '2', e.g. for ancestral and derived allele (or major and minor). The FSTAT format is described in the manual on pp.73-74 (don't use '0' to code your alleles). The two alleles at one locus are provided as a single "number": 12, 11, 22, or 21, first position (left-most) is for first allele, second position (right-most) is for second allele.

The procedure to import data from an external text file is described in section 3.2.2 in the manual, see parameter 'source_file_type'.

Using an FSTAT file means you have to use the neutral trait for your simulation. Check the example files in the "example" folder of the distribution package. You'll find the example 'fstat_input_and_cross.ini' to read in an FSTAT-formatted file for neutral markers, and then run a simulation from it. The example runs on data files generated from the simulations in the Nemo2.ini file in the same folder. The FSTAT format is the only used to read data for the neutral markers for now.

I hope this helps

Cheers

Fred