Code to reproduce results from Yardeni et al., preprint This was used to generate whole-genome phylogenomics and infer hybridization in Tillandsia subgenus Tillandsia.
- raw_to_vcf_GATK.md - processing BAM files to VCF calls and filtering.
- KING_analysis.sh - short script to infer kinship coefficients with KING
- ASTAL_gene_trees_wins.sh - script to generate VCF for genomic intervals and infer a species tree with ASTRAL
- example_plot_mod_180121.R - script to create Twisst plots, modified slightly from original
- plot_twisst_mod.R - modified Twisst functions
- iqtree.sh - generic script to produce trees with iqtree2
- makewindows.sh - generic trees to infer ML trees on genomic windows from a VCF file.