ima2 help please

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Oct 20, 2015, 2:38:50 AM10/20/15
to Isolation with Migration
Hello everyone,
Since several month I am trying to analyze my dataset to infer migration rates between three human populations analyzing hvr-1 locus.
I have found many problems to understand how set the parameter.
Can you help me please?
In the input file i wrote these lines before my sequences

# Test_1
A B C 
locus_hvr1 115 269 191 360 H 0.25 0.00012

It is correct the mutation rate?
I want to test 0.003 mutational events per locus per generation, considering 25 years per generation.

Then, moving to consider the command line, I want to understand the migration rate between these three populations knowing that these were separated 700 years before present.

mpirun -np 6 .IMa2p -i ./test1.txt -o ./test1_output.txt 
-b 10000000   
-l 10000 
-d 1000 
-hf 1 
-hn 1 
-hk 1 
-u 25  
-t 0.084  ##Is ti correct???? (700/25)*0.003
-m 333  ##Is ti correct???? 1/0.003
-q 6000 ##Is ti correct???? 4*500000*0.003

Do you need other information to help me?
Thank you very much

Fastinc Documentation

Oct 29, 2015, 1:12:25 PM10/29/15
to Isolation with Migration
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