Config
This folder contains the configuration files necessary for running the demographic models M1-M6 mentioned in the bioRxiv draft and for converting files in pseudo_MS format into the cbSFS (also used in the draft).
Running models M1-M6
Here we are assuming 2 diploid samples/population (which is also applicable to 4 haploid samples/population), block sizes of 2Kb and the working directory is that in which the ABLE binary is situated. The corresponding command lines for launching these models have been provided below.
N.B. In order to run these very same command lines on the 500bp data provided in the data folder, you need to replace -r tbi2 2001 by -r tbi2 501 and change the filename for the datafile keyword in the respective config file.
M1
./ABLE 8 xxx -t tbi1 -r tbi2 2001 -I 2 4 4 -ej tbi3 1 2 -T config_M1.txt
M2
./ABLE 8 xxx -t tbi1 -r tbi2 2001 -I 2 4 4 -n 1 tbi4 -n 2 tbi5 -ej tbi3 1 2 -T config_M2.txt
M3
./ABLE 8 xxx -t tbi1 -r tbi2 2001 -I 2 4 4 -n 1 tbi4 -n 2 tbi5 -g 1 tbi6 -g 2 tbi7 -ej tbi3 1 2 -T config_M3.txt
M4
./ABLE 8 xxx -t tbi1 -r tbi2 2001 -I 2 4 4 -n 1 tbi4 -n 2 tbi5 -m 1 2 tbi6 -m 2 1 tbi7 -ej tbi3 1 2 -T config_M4.txt
M5
./ABLE 8 xxx -t tbi1 -r tbi2 2001 -I 2 4 4 -n 1 tbi4 -n 2 tbi5 -em tbi8 1 2 tbi6 -em tbi8 2 1 tbi7 -ej tbi3 1 2 -T config_M5.txt
M6
./ABLE 8 xxx -t tbi1 -r tbi2 2001 -I 2 4 4 -n 1 tbi4 -n 2 tbi5 -es tbi8 1 tbi6 -ej tbi8 3 2 -es tbi8 2 tbi7 -ej tbi8 4 1 -ej tbi3 1 2 -T config_M6.txt
Converting files from pseudo_MS format to the bSFS
The following command lines along with the provided config files can be used to produce the bSFS input used in the paper (which is also available in the data folder).
./ABLE config_bSFS_Pongo_500bp.txt
./ABLE config_bSFS_Pongo_2kb.txt
Converting files from pseudo_MS format to the cbSFS (composite bSFS)
The following command lines along with the provided config files can be used to produce the cbSFS input used in the paper (which is also available in the data folder).
./ABLE config_cbSFS_Pongo_500bp.txt
./ABLE config_cbSFS_Pongo_2kb.txt