DILS_3pop_SNP

Version 1.0.0 of DILS_3pop_SNP used in Le Roy et. al. (2021)[https://doi.org/10.1038/s41467-021-27549-1]. This is a modified version of DILS:

1. taking fasta file as input (ex: Morpho_Peru_dils.fa. in /data)
2. investigate models of divergence with/without gene flow for 3 species/populations.
3. designed for RAD datasets, by conditionning the mutations on the observed number of SNPs and not on the mutation rate.
   To adapt to your project, the best is to set a single directory where all analysis (different projects for different species, etc ...) will be conducted.
   Let's name this directory projectpath The path to such projectpath has to be specified in the Snakefile (named here Snakefile_3pop).

in DILS_3pop.sh

line 11
binpath='' # full link to the bin directory of the DILSmcsnp depository

in Snakefile_3pop

lines 44 and 47
binpath='' # full path to the bin directory of the DILSmcsnp depository
projectpath= '' # full path to the directory where all DILS analysis will be performed, i.e, where yaml files have to be placed

in yaml file

infile: # full path to the fasta file, placed within the projectpath
config_yaml: # full path to the current yaml file