Code for comparative genomics manuscript, including genome assemblies, annotations and subsequent analyses
genome_assemblies: assembly pipeline for C. incerta, C. schloesseri, and E. debayana
repeat_masking: repeat masking pipeline prior to gene model annotation
gene_annotation: gene model annotation pipeline
phylogenetic_analyses: IQ-TREE and ASTRAL-III analyses
synteny_analysis: identification of synteny blocks using SynChro
Orthofinder_coreR: Orthofinder run and gene family analyses for 6 core-Reinhardtinia species
Cactus_WGA: whole-genome alignment pipeline
phastCons: pipeline for identification of conserved elements from Cactus alignment