Code and data underlying the manuscript by van der Heijden et al. on Mechanitis and Melinaea butterfly diversification.

https://www.biorxiv.org/content/10.1101/2024.07.07.602206v1

Processing of raw reads

• Snakemake file 1
• Snakemake file 2

Figure 1:

• Nuclear and mitochondrial phylogenetic tree
• R script to plot the co-phylogeny

Figure 2:

• Calibrated tree
• R script to plot the distribution maps
• DSuite analysis
• TWISST and WindowTree concordance factor

Figure 3:

• Bash script to generate the genome scans with PBS and fd
• R script to plot the genome scans
• Underlying data: Fst and Dxy values, introgression values and PBS values

Figure 4:

• R script to filter BUSCO output
• R script for preliminary synteny ribbon plot
• R script for refined synteny ribbon plot
• R script to calculate and plot rearrangements
• R script to detect breakpoints in Mechanitis and Melinaea
• R script to plot genomescans with breakpoints and boxplots Mech
• R script to plot genomescans with breakpoints and boxplots Mel