setting the parmfile

[Ioana Brännström]

Hi Petter,

I am starting to use migrate and after playing with your tutorials I have started to work with my own data. I am using your Migrate 4.2.7

I have a DNA sequence dataset of 3 loci and I would like to consider different substitution rates for each of them. I really got sucked because I do not know how to set my parmfile and infile for three loci. I have a concatenated dataset with two populations. I am entering the "  DATATYPE AND DATA SPECIFIC OPTIONS" menu and there I can choose this options: 

1. Change mutation model

5. One category site

6. One region of substitutions rates.

I am thinking that I am on the right place to change so I should choose option 6 and three regions. Here I got sucked because I am not sure how to proceed. I assume somewhere I need to give the coordinates for my loci

I try to search the answer how to set the parmfile but I was not able to find it. It will be so great if you could help. I am attaching my infile as it is now. Maybe here I need to change something.

Best

regards,

Ioana

[Peter Beerli]

Ioanna,

unfortunately you cannot assign different site-rates to different loci (this is planned but never bubbled up as one of the very important things)

I would assign site rate variation anyway because that will allow your sites to vary (which will be similar to your intended effect).

If you have independent 3 loci you definitely should treat them like that (tell migrate that there are 3 loci!

For example for 2 population 3 loci problem (with concatenated sequences this could look like this

2 3 exampledata

(s1200) (s1500) (s1300)

10 fist population

….. etc

Peter

PS. be also aware that the 4.2 series is not officially out of the gate (I wrestling with some details in the manuscript)

   

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