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ABC_GWH

A cookbook to study Genome Wide Heterogeneity in introgression rates

The proposed recipe is largely inspired by previous studies by Jeffrey Ross-Ibarra, who was one of the first persons to democratize ABC analysis by sharing many powerful source-codes .... and by kindly replying to unbearable emails like mine.


In this cookbook, we do not pretend to offer the most efficient solution to conduct general investigations based on ABC, as some excellent alternatives made by clever people are already available. I personally suggest to everyone interested in historical inference (and therefore in ABC) to have a look at DIYABCand ABCtoolBox. If you are motivated, you can also try to deal with DaDi (and if you succeed, please do send me an email to tell me how you did!).


Before we start cooking, I would like to talk a little bit about my kitchen. It's a nice Unix-like kitchen called Ubuntu. Like many single men, I do not change my ways easily, so I cannot help people who have adopted some too complicated systems for me (Windows for example).

 

The first part of this cookbook mainly describes three utensils. Because these utensils may be a little tricky to use, you can see below a tutorial. If you read it seriously, you should understand how the three softwares priorgen, msnsam and mscalc work.

The following lines of command may appear obscure to you if you have not read the tutorial. Otherwise, you should find them helpful :

iso (=SI):

msnsam tbs nsims -t tbs -r tbs tbs -I 2 tbs tbs 0 -m 1 2 tbs -m 2 1 tbs -n 1 tbs -n 2 tbs -ej tbs 2 1 -eN tbs tbs

 

island (=SC) :

msnsam tbs nsims -t tbs -r tbs tbs -I 2 tbs tbs 0 -m 1 2 tbs -m 2 1 tbs -n 1 tbs -n 2 tbs -ej tbs 2 1 -eN tbs tbs

 

sym (=AM):

msnsam tbs nsims -t tbs -r tbs tbs -I 2 tbs tbs 0 -m 1 2 0 -m 2 1 0 -n 1 tbs -n 2 tbs -ema tbs 2 0 tbs tbs 0 -ej tbs 2 1 -eN tbs tbs

 

allo (=SC):

msnsam tbs nsims -t tbs -r tbs tbs -I 2 tbs tbs 0 -m 1 2 tbs -m 2 1 tbs -n 1 tbs -n 2 tbs -eM tbs 0 -ej tbs 2 1 -eN tbs tbs

 

 

Obviously, I also strongly encourage everyone to read the manual for MS to draw your own models and release your creativity.


In the 'Utensils' menu you will find the sources for each script and some related information.

 

Finally, I would like to take this opportunity to challenge motivated and skilled PhD-students : if one ever visits this website, please go here