ima2 help please

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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

3 

A B C 

((1,2):3,0):4

1

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 

-j3 

-p234578 

-r2 

-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

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