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GeneratingHaplotypesWithFastsimcoal

Robert Kofler Christos Vlachos

1 Introduction

As an input MimicrEE2 requires haplotypes. Ideally this haplotypes would be derived from sequencing multiple individual of a population for the organism of interest.
However such extensive sequence data will frequently not be available for many organisms. Thus one elegant solution is to simulate the input haplotypes.
One very useful tool for simulating haplotypes is fastsimcoal http://cmpg.unibe.ch/software/fastsimcoal2/
This tool allows to simulate haplotypes under complex evolutionary scenarios.
MimicrEE2 allows converting the output of fastsimcoal (.arp files) into the haplotype format supported by MimicrEE2.

2 Haplotypes for a single chromosome

run fastsimcoal to obtain .arp files

First its necessary to generate one of the input files for fastsimcoal such as a .par file (contains the parameters for the evolutionary scenarios that should be simulated).
For details see the fastsimcoal manual http://cmpg.unibe.ch/software/fastsimcoal2/

In this walkthrough we use the following par file https://sourceforge.net/projects/mimicree2/files/fastsimcoal/20kb-chr1.txt/

Than we run fastsimcoal with the command:

fsc26 -i 20kb-chr1.txt -n 1 -q

We obtain an arp-file such as the following: https://sourceforge.net/projects/mimicree2/files/fastsimcoal/20kb-chr1_1_1.arp

convert arp files into haplotype file (diploids)

Finally we may convert this file (20kb-chr1_1_1.arp) into a MimicrEE2 haplotype file; To obtain diploid haplotypes we use the following command:

java -jar mim2.jar arp2mimhap --chrname 2L --input 20kb-chr1_1_1.arp --output chr2L.mimhap

Which yields the following haplotype file: https://sourceforge.net/projects/mimicree2/files/fastsimcoal/chr2L.mimhap.gz/download

An example of the first ten lines:

2L  174 A   A/T AA AA AA AT AA AA TA AT AT AA AA AA TA TA AA TA AA AA TA AA AA AA TT AT TA AA AA AA AT AA AT AA TA AA AA AA TA AA AA TT AT AA TA AA AA AA AA TA AA AA TA AA AT AA AT TA AA AA AA AT TA AA AA AA AA AT AA AA TA AA TA AA AT TA AA TT AA AA AA AA AA AA AT AT TA AA TA AT AA AA AA AA AT AA AT TA AA AA AA AA AA AA AA AA AA AA AA AA AA TA AA AA AA AA TT AA TA AA AA AT AA AA AA AA TA AA AA AA AA AA AA AA AA AT AA AA AA AT AA AA AA AA AA AA AA AT TA TA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AT AA AA AT AT AT AA AA AT TA AA AA AA TA AA AA AA AA AA AT AA AA AT AA AA AA AA AA TA AA AA AA AA AA TA AT AA AA AT AA AA AA TA AA AA AT AT AA AA AA AA AA AT AT AA AA TA AT AA AT AA AT AA AA AT TA AT AA AA AA AA AA AA AA AA AA AA AA AA AA AT AA AA AA AA TA AT AA AA AA AA TA AA AA AA AA AA AA AA AA AA AT AA AA AA AA TA AA AA AA AT AA AT AT AT AA AA AA AA AA AT AA AA AA AT AA AA TA AA AA AA AA TA AT TA AA AA AT TA AA AA AA AA AT AA AA AA AA AA AA TA TT TA TA AA AA AT TT AT AA AA AA TT AA AA TA AA AA AA AA AA AA AA AA TA AA AT AA TA AA AA AT AA AT AA AA TT TA AA AT AA AA AA TA AA AA AA AA AA AA AA AT AT AA AT AT AA TT AA AA AA AA AA TT AA TA AT AA TA AA AT TT AA TA AA AA AT AA AT AT AA AA AA AA AT TT AA AT AT AA AA AT AT AA AA TA AA AT TA TT TT TA AA AT TA AT TA AA AA AA AA AA TA AT AA AA AA AA AA AA AA AA AA AT AA AA AA AA TA TA AA AA AA AA AA AA AA AA AA TA AA AA AA AA TA AA AA AA AA AA AA TT AA TA TA AA AA AA AA AA AA AA AA AA AA AA TA AT AA AT AA TT AA AA AA AT AA AT AA AA TA AA AA AA TT
2L  685 G   G/C GG GG GG GG GG GG GC GG CG GG CG GG GG GG GG GG GC GC GG GG GC GG GG GG GG GC CG CG CG GC GG CG GG GG GG GG GG GC GC GG GG CG GC CG GC GC GC GC CC GC GG GG GG CG GG GC GG GC GG CG GC CG CG GG GC GG GG GG GG CC GG GG GG GC GG GG CG CG CC GG CG GG GG GG GG GC GC CG GC CG GG GG CG GG GG GG GC GC GG GG GG GG GG CG GC GC GC GC CC GG CC CC CG CC GG CG GG CC CG CG CC GG CG GC GC CC GC GG CG GC GG CG GG CG CC GC GC GG GC GC GC GC GG GG GG GG GG GC GC CC GG GG GG GG CG GG GC GG GG GG GG GG GG CG GG GG GC CG GG GG CG GG GG CG GC CC CG GC GG GC GG CC CC GG CG CG CG GG CG CG GG CC GG GG CG GC CG CG GG GG GG CG CC CG GC CG GG GG GG CC GG CG GG GG CC GC CC GG GG CG GG GG CG GG GG GG CG GG GG GG GG GG GG GG GG GG GC GG GC GG GC CC GC CG CG GG GG GG GG GG GG GG GG GC GG GG GG GG GG GC CG GG GG CG GG GG GG GG GG CC CG GC GG CG GG GG GC GG GG CG GG GC CG GG GG CG GG GG CC GG CG GG GG GC GC GC GC GG GG GG GG CG GG GG GG GG CG GG GG GG GG GG CG CG CG GC GG GC GG GG CG CG GG CG CC GC GG GG GG GG GG GC GG CC CG CC CG CG GG GG CG GG GG GG GC GG GG GC CG GC CC GG GC CG CG CC GG GG GG GG GG GC GG GG GC GG GG CG CG GG GG GG GG GG CG CC GG CG GG GC GG CG GC GG GG GG GG CG GG CG GC GG GG GG CG GC GC GG GG GG GG CG GG CG GG GC CG GG GG GG GC CC CG GG GG GG GG GG GG GG GG GG GC CG GG CG GG GG CG GG CC GG GG CG GG GG GG CG CG GG GG GG CG GG GG GG GG CG CG GC CG GG GG CC GC CG GG GG GG GG GG GG CC GG CC GG GG GG GC GG GG GG GC GG CG GG CG GG CG GG GC GG GG GG GG GG GG GC GG GG GG CG GG GC CC GG CC GG GG GG
2L  692 A   A/C AC CA CA CA CA CC AC CA CA CA CA AA AC AC AA AC AC AC AC AA CC AC AA CA AA AC CC CC CA AC AA CC AC CC CA AA AA CC AC AA AA CC AC CA CC AC AC AC CC AC AA CA AA CC AA AC CC AC AA CA AC CC CC AA AC AA CA CA AA CC AC CA AA AC AC AA CA CC CC CA CA AA AA CA AA AC AC CA CC CA CA CC CA AC AA AC CC AC AC AC AA AC AA CA CC AC AC CC CC AA CC CC CA CC AA CA AA CC CC CA CC CC CA CC AC CC AC AA CC AC CC CC AA CA CC AC CC AA CC CC CC AC AC CA AA AA AC AC AC CC AA CA AC AC CC AA AC AC AC CC AA CC AC CC AC AA CC CA AA AA CA CA CC CA AC CC CA AC AA AC AA CC CC AC CA CC CA AA CA CA CA CC AC AA CC CC CC CC CA AA CA CC CC CA CC CA AC AA CC CC AA CA AA AA CC CC CC CA CA CA AA AA CA AC AA AA CA AC CA CA AC CA CC AA AA AA CC AC AC AA AC CC AC CC CC AA AA CC CC CC AC AA AA AC CA AC AA CC AA CC CC AA AC CC CC AC AA AC CC CC CA AC AC CA AC CA AC CA CA CA AC AC CA CC AC CA CA AC CC CA CA AC AA AC AC AC CC AA CA AA AC CA CA AC CC CA CC AA CA AC CA AA CA CC CC AC AA AC AC AC CA CA AA CA CC AC CA AA AA CA AC CC AA CC CA CC CC CC AA AC CC CA AA AA CC AC CA AC CA CC CC AA AC CA CA CC AA AA AC AC AA CC AC CA AC AA CA CA CC CA CA AC AA CC CC CC AC CA AA AC AC CA AC AC AA CA AA CC AA CA CC AA CC AA CA CC CC CA AA CA AA CC AA CA CC AC CA AA AA CA AC CC CA AC AA AA AA AA AA AC AA AC AC CC CA CC AA AA CA CC CC AC CA CC CC AA AA CC CA AA AA CC CA AA AA CC AC CC CC CC CC AA AC CC AC CA AA CC AC AA CC CA CC CC CC CA AA AA AC AA AC AC CC CA CA CA CA AA CC AC CC AA CA CC AA CA AA AC AC AA CA CC CA AC CC AA CC CA AC AA
2L  729 C   C/T CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC TC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
2L  833 A   A/C AC CA CA CA CA CC AA CA AA CA AA AA AC AC AA AC AA AA AC AA CA AA AA CA AA AA AA AA AA AA AA AC AC CC CA AA AA AA AA AA AA AC AA AA CA AA AA AA AA AA AA CA AA AC AA AA AC AA AA AA AA AC AC AA AA AA CA CA AA AA AC CA AA AA AC AA AA AC AA CA AA AA AA CA AA AA AA AA CA AA CA CC AA AC AA AC CA AA AC AC AA AC AA AA CA AA AA CA AA AA AA AA AA AA AA AA AA AA AC AA AA CC AA CA AA AA AA AA AC AA CC AC AA AA AA AA CA AA CA CA CA AA AC CA AA AA AC AA AA AA AA AA AC AC AC AA AA AC AC CC AA CC AA AC AA AA CA AA AA AA AA CA CC AA AA AA AA AA AA AA AA AA AA AC AA AA AA AA AA AA CA AA AC AA AC CA AC AC CA AA CA AC AA AA AA AA AC AA CA AA AA AA AA AA AA CA AA CA CA AA AA AA AA AA AA AA AA AC CA AA AC CA CA AA AA AA CA AC AA AA AA AA AA AA AC AA AA CC CA CC AC AA AA AA CA AC AA CC AA CA AA AA AC AC CC AC AA AC CC AA AA AA AC AA AC CA AA CA CA AA AC AA AA CC AA AA AA AC AA CA AA AC AA AA AA AA CA AA CA AA AC AA CA AC CC CA AC AA CA AC CA AA AA AC AC AA AA AA AC AC AA AA AA AA AA AA CA AA AA CA AC AA AA AA AA AA AA AC AA AC AC CA AA AA CA AC CA AA AA CA AA AA AA AA AA AA AA AA AC AC AA CA AC CA AA AA AA AA AC CA CA AC AA CA AC AA AC AA AA AA AC AA AA AA AA CA AA AC AA AA CA AA CC AA AA CA CA AA AA CA AA AC AA AA CA AA AA AA AA AA AA AA AA AC AA AA AA AA AA AC AA AC AA AC CA AC AA AA AA CC AA AC CA AC CC AA AA AC AA AA AA CC AA AA AA CC AC AC AC CA AC AA AC AA AA AA AA CC AC AA CC CA AA CA AA CA AA AA AA AA AA AA CA CA AA CA AA AA AC AC CA AA CA CC AA CA AA AA AC AA CA AC CA AA AA AA AA CA AC AA
2L  1023    A   A/C AA AA AA AC AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA CA AA AA AA AA AA AA AA AC AA AA AA AA AA CA AA AA AA AA AA CA AA AA AA AA CA AA AA AA AA AA AA AA CA AA AA AA AA AA AA AA AA AA AA AA AA AA AA CA AA AA AA AA AA AA AA AA AA AA AA AA AA CA AA CA AA AA AA AA AA AA AA AA CA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA CA AA AA AA AA AA AA AA AA AA AA AA AA AC AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AC AA AA AA AC AA AA AA AA AA AA AA AA AA AA AA AA AA AA AC AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AC AC AA AA AA AA AA AA AC AA AA CA AA AA AC AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA CA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA CA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AC AA AA AA AA AA AC AA AA AA AA AA AA AA AA AA AA AA AA AA AC AC AA AA AA CA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA CA AA AA AA AA AA AA AA CC AA AA AC AA AA AA CA AA AA AA AA AA AA AA AA AC AA AA AC AA AA AA AA AA AA AA AA AA CA AA AA AA AA AA CA AA CA AA AA AC AA AA AA AA AA AA AA AA CA AA AC AC AA AA AA AA AA AA CA AA AA CA CA AC CA AA AC AA AC CA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA CA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AC AA AA AA AA AA AC AA AC AA AA AA AA AA AA AA
2L  1117    A   A/T AA AA AA AA AA AA AA AA AA AA AA AA TA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
2L  1400    T   T/G TG TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT GT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT GT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TG TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT GT TT TT GT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TG TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT
2L  1444    A   A/T AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AT AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AT AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA TA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AT AA AA AA AA AA AA AA AA AT AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
2L  1515    T   T/C TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TC TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TC TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TC TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TC TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TC TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TC TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TC TT TT TT TT TT TT TC TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT

convert arp files into a haplotype file (haploids)

To convert the arp file into a haplotype file for haploids the following command may be used

java -jar mim2.jar arp2mimhap --chrname 2L --input 20kb-chr1_1_1.arp --output chr2L-haploid.mimhap --haploid

This gives the following output https://sourceforge.net/projects/mimicree2/files/fastsimcoal/chr2L-haploid.mimhap.gz/download

And an example of the first ten lines

2L  174 A   A/T AA A A A A A A T A A A A T A A T A T A A A A A A T A T A A A T A A A A A T A A A A A A A T T A T T A A A A A A A A T A A A T A A T A A A A A A A T A A A A A T T A T A A T A A A A A A A A A T A A A A A T A A A A T A A A T T A A A A A A A A T T A A A A A A A A A A T A A A A T A A A T A A A A T T A A A T T A A A A A A A A A A A A A T A T T A A A T A A T A A A A A A A A A T A A A T T A A A A A A A A A A A A A A A A A A A A A A A A A A A T A A A A A A A A A T T A A T A A A A A A T A A A A A A A A T A A A A A A A A A A A A A A A A A A T A A A A A A A T A A A A A A A A A A A A A A A T T A T A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A T A A A A A T A T A T A A A A A T T A A A A A A A T A A A A A A A A A A A A T A A A A A T A A A A A A A A A A T A A A A A A A A A A A T A A T A A A A A T A A A A A A T A A A A A A T A T A A A A A A A A A A A T A T A A A A T A A T A A A T A A A T A A A A A T T A A T A A A A A A A A A A A A A A A A A A A A A A A A A A A T A A A A A A A A T A A T A A A A A A A A T A A A A A A A A A A A A A A A A A A A A T A A A A A A A A T A A A A A A A A T A A A T A T A T A A A A A A A A A A A T A A A A A A A T A A A A T A A A A A A A A A T A A T T A A A A A A T T A A A A A A A A A A T A A A A A A A A A A A A T A T T T A T A A A A A A T T T A T A A A A A A T T A A A A T A A A A A A A A A A A A A A A A A T A A A A T A A T A A A A A A T A A A T A A A A T T T A A A A T A A A A A A T A A A A A A A A A A A A A A A A T A T A A A T A T A A T T A A A A A A A A A A T T A A T A A T A A T A A A A T T T A A T A A A A A A T A A A T A T A A A A A A A A A T T T A A A T A T A A A A A T A T A A A A T A A A A T T A T T T T T A A A A T T A A T T A A A A A A A A A A A T A A T A A A A A A A A A A A A A A A A A A A T A A A A A A A A T A T A A A A A A A A A A A A A A A A A A A T A A A A A A A A A T A A A A A A A A A A A A A T T A A T A T A A A A A A A A A A A A A A A A A A A A A A A T A A T A A A T A A T T A A A A A A A T A A A T A A A A T A A A A A A A T T
2L  685 G   G/C GG G G G G G G G G G G G G C G G C G G G C G G G G G G G G G G G G C G C G G G G G C G G G G G G G G G C C G C G C G G C G G C G G G G G G G G G G G G C G C G G G G C G G C C G G C G C G C G C C C G C G G G G G G C G G G G C G G G C G G C G G C C G C G G G G C G G G G G G G G C C G G G G G G G C G G G G C G C G C C G G C G G G G G G G G G G C G C C G G C C G G G G G C G G G G G G G G C G C G G G G G G G G G G C G G C G C G C G C C C G G C C C C C G C C G G C G G G C C C G C G C C G G C G G C G C C C G C G G C G G C G G C G G G C G C C G C G C G G G C G C G C G C G G G G G G G G G G G C G C C C G G G G G G G G C G G G G C G G G G G G G G G G G G C G G G G G G C C G G G G G C G G G G G C G G C C C C G G C G G G C G G C C C C G G C G C G C G G G C G C G G G C C G G G G C G G C C G C G G G G G G G C G C C C G G C C G G G G G G G C C G G C G G G G G C C G C C C G G G G C G G G G G C G G G G G G G C G G G G G G G G G G G G G G G G G G G G C G G G C G G G C C C G C C G C G G G G G G G G G G G G G G G G G G C G G G G G G G G G G G C C G G G G G C G G G G G G G G G G G C C C G G C G G C G G G G G G C G G G G C G G G G C C G G G G G C G G G G G C C G G C G G G G G G C G C G C G C G G G G G G G G C G G G G G G G G G C G G G G G G G G G G G C G C G C G G C G G G C G G G G C G C G G G C G C C G C G G G G G G G G G G G C G G C C C G C C C G C G G G G G C G G G G G G G G C G G G G G C C G G C C C G G G C C G C G C C G G G G G G G G G G G C G G G G G C G G G G C G C G G G G G G G G G G G C G C C G G C G G G G C G G C G G C G G G G G G G G C G G G C G G C G G G G G G C G G C G C G G G G G G G G C G G G C G G G G C C G G G G G G G G C C C C G G G G G G G G G G G G G G G G G G G G C C G G G C G G G G G C G G G C C G G G G C G G G G G G G C G C G G G G G G G C G G G G G G G G G C G C G G C C G G G G G C C G C C G G G G G G G G G G G G G C C G G C C G G G G G G G C G G G G G G G C G G C G G G C G G G C G G G G C G G G G G G G G G G G G G C G G G G G G C G G G G C C C G G C C G G G G G G
2L  692 A   A/C AA C C A C A C A C A C C A C C A C A C A C A A A A C A C A A A C A C A C A C A A C C A C A A C A A A A C C C C C C A A C A A C C A C C C C A A A A A C C A C A A A A C C A C C A C C A C A C A C C C A C A A C A A A C C A A A C C C A C A A C A A C C C C C A A A C A A C A C A A A C C A C C A A A A C A C A A C A C C C C C A C A A A A A C A A A A C A C C A C C C A C A C C C A A C A A A C C C A C A C A C A A A C A A C A C C A C A C C C C C A A C C C C C A C C A A C A A A C C C C C A C C C C C A C C A C C C A C A A C C A C C C C C A A C A C C A C C C A A C C C C C C A C A C C A A A A A A C A C A C C C A A C A A C A C C C A A A C A C A C C C A A C C A C C C A C A A C C C A A A A A C A C A C C C A A C C C C A A C A A A C A A C C C C A C C A C C C A A A C A C A C A C C A C A A C C C C C C C C C A A A C A C C C C C A C C C A A C A A C C C C A A C A A A A A C C C C C C C A C A C A A A A A C A A C A A A A C A A C C A C A A C C A C C A A A A A A C C A C A C A A A C C C A C C C C C A A A A C C C C C C A C A A A A A C C A A C A A C C A A C C C C A A A C C C C C A C A A A C C C C C C A A C A C C A A C C A A C C A C A C A A C A C C A C C A C C A C A A C C C C A C A A C A A A C A C A C C C A A C A A A A C C A C A A C C C C A C C A A C A A C C A A A C A C C C C A C A A A C A C A C C A C A A A C A C C A C C A A A A A C A A C C C A A C C C A C C C C C C A A A C C C C A A A A A C C A C C A A C C A C C C C A A A C C A C A C C A A A A A C A C A A C C A C C A A C A A C A C A C C C A C A A C A A C C C C C C A C C A A A A C A C C A A C A C A A C A A A C C A A C A C C A A C C A A C A C C C C C A A A C A A A C C A A C A C C A C C A A A A A C A A C C C C A A C A A A A A A A A A A A C A A A C A C C C C A C C A A A A C A C C C C A C C A C C C C A A A A C C C A A A A A C C C A A A A A C C A C C C C C C C C C A A A C C C A C C A A A C C A C A A C C C A C C C C C C C A A A A A A C A A A C A C C C C A C A C A C A A A C C A C C C A A C A C C A A C A A A A C A C A A C A C C C A A C C C A A C C C A A C A A
2L  729 C   C/T CC C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C T C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C T C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C
2L  833 A   A/C AA C C A C A C A C A C C A A C A A A C A A A A A A C A C A A A C A A A A A C A A C A A A A A C A A A A A A A A A A A A A A A A C A C C C C A A A A A A A A A A A A A A C A A A A C A A A A A A A A A A A A A C A A A A C A A A A A C A A A A A A A A A C A C A A A A A A C A C A A A A A A C C A A A A A A C A A A A A C A A C A A A A A A A C A A A A A A A A A C A A A C A C C A A A C A A A C C A A A A C A C A A A C A A A A C A A A A A C A A A A A A A A A A A A A A A A A A A A A A C A A A A C C A A C A A A A A A A A A A C A A C C A C A A A A A A A A C A A A C A C A C A A A A C C A A A A A A C A A A A A A A A A A A C A C A C A A A A A C A C C C A A C C A A A C A A A A C A A A A A A A A A C A C C A A A A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A A C A A A A C A A A C C A A C A C C A A A C A A C A A A A A A A A A C A A C A A A A A A A A A A A A A C A A A C A C A A A A A A A A A A A A A A A A A A C C A A A A C C A C A A A A A A A C A A C A A A A A A A A A A A A A C A A A A C C C A C C A C A A A A A A C A A C A A C C A A C A A A A A A C A C C C A C A A A C C C A A A A A A A C A A A C C A A A C A C A A A A C A A A A C C A A A A A A A C A A C A A A A C A A A A A A A A C A A A C A A A A C A A C A A C C C C A A C A A C A A C C A A A A A A C A C A A A A A A A C A C A A A A A A A A A A A A C A A A A A C A A C A A A A A A A A A A A A A C A A A C A C C A A A A A C A A C C A A A A A C A A A A A A A A A A A A A A A A A A C A C A A C A A C C A A A A A A A A A A C C A C A A C A A C A A C A A A C A A A A A A A C A A A A A A A A C A A A A C A A A A C A A A C C A A A A C A C A A A A A C A A A A C A A A A C A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A C A A A C A A A C C A A C A A A A A A C C A A A C C A A C C C A A A A A C A A A A A A C C A A A A A A C C A C A C A C C A A C A A A C A A A A A A A A C C A C A A C C C A A A C A A A C A A A A A A A A A A A A A C A C A A A C A A A A A A C A C C A A A C A C C A A C A A A A A A C A A C A A C C A A A A A A A A A C A A C A A
2L  1023    A   A/C AA A A A A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A A A A A A C A A A A A A A A A A C A A A A A A A A A A A C A A A A A A A A A C A A A A A A A A A A A A A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A C A A A A A A A A A A A A A A A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A A A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A C A C A A A A A A A A A A A A A C A A A A C A A A A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A A C A C A A A A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A A A A A C C A A A A A C A A A A A A C A A A A A A A A A A A A A A A A A A C A A A A A C A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A C A A A C A A A A A A C A A A A A A A A A A A A A A A A C A A A A C A C A A A A A A A A A A A A C A A A A A C A C A A C C A A A A C A A A C C A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A C A A A C A A A A A A A A A A A A A A
2L  1117    A   A/T AA A A A A A A A A A A A A A A A A A A A A A A A T A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A
2L  1400    T   T/G TT G T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T G T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T G T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T G T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T G T T T T T G T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T G T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T
2L  1444    A   A/T AA A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A T A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A T A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A T A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A T A A A A A A A A A A A A A A A A A T A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A
2L  1515    T   T/C TT T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T T T T T T T T T T T C T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T

3 Haplotypes for multiple chromosomes

In order to obtain haplotypes for multiple chromosomes we recommend to simulating the haplotypes for each chromosome separately and concatenating the MimicrEE2 haplotypes.

Given the two par files (fastimcoal paramters)

We run fastsimcoal twice

fsc26 -i walkthrough/20kb-chr1.txt -n 1 -q
fsc26 -i walkthrough/20kb-chr2.txt -n 1 -q

Than convert both chromosomes independently with MimicrEE2

java -jar mim2.jar arp2mimhap --chrname 2L --input 20kb-chr1_1_1.arp --output chr2L.mimhap
java -jar mim2.jar arp2mimhap --chrname 3R --input 20kb-chr1_1_1.arp --output chr3R.mimhap

And finally simply concatenate the results

gzip -cd chr2L.mimhap.gz chr3R.mimhap.gz| gzip -c > combined2L_3R.mimhap.gz

which yields the following file https://sourceforge.net/projects/mimicree2/files/fastsimcoal/combined2L_3R.mimhap.gz/download

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