Commands and scripts for "Incomplete recombination suppression fuels extensive haplotype diversity in a butterfly color pattern supergene": simonhmartin/Danaus_supergene_diversity_2025: v1.0.0

simonhmartin/Danaus_supergene_diversity_2025: v1.0.0

Commands and scripts for "Incomplete recombination suppression fuels extensive haplotype diversity in a butterfly color pattern supergene", De-Kayne et al. 2025 PLOS Biology
The following analyses presented in the final paper are detailed as follows:

Distribution maps (Figure 1A): Distribution_maps
Read alignemnt and bam filtering: Mapping_reads
Indel realignment: other_analysis_scripts
Genotype calling and filtering: other_analysis_scripts
Phasing: phasing
PCA (Figure S1A): other_analysis_scripts
GWAS (Figure 1C-D, S1B-C): other_analysis_scripts
Neighbor-Net (Figure 2A): NeighborNet_network
ADMIXTURE (Figure 2A, 2B, S1D, E-H): other_analysis_scripts, Plot_Admixture_pies
Popgen window statistics (Figure 3): other_analysis_scripts
Ancestry painting (Figure 2C, 4B, 4D, S1I, S1I-K): distPaint, Loter
Topology weighting (Figure 4A, 4C, S1L): Twisst2
LD heatmaps (Figure S1M): other_analysis_scripts
gIMble (Table S2, Figure S1N): other_analysis_scripts

MIT License