Scripts associated to the paper: 'Selfing Siberian Arabidopsis lyrata is a progenitor of the allopolyploid Arabidopsis kamchatica'.
PiW: Calculation of nucleotide diversity in 10 Kb windows.
CoGe processing: Working with output of Synmap = synteny analysis of online platform CoGe: https://genomevolution.org/coge/SynMap.pl
- step 1: transforming output to separate files containing start and end of each syntenic block, performed on command line.
- step 2: merging starts and ends to create following file format: chrA, startA, endA, chrB, startB, endB. A and B depict two different genome assemblies.
- step 3: Visualizing the result in R using the library circlize.
Demographic_modeling: contains .est and .tpl file for Fastsimcoal, plus input sfs and script used to generate parameter estimates.