Comparative genomics of Chlamydomonas

Code for comparative genomics manuscript, including genome assemblies, annotations and subsequent analyses

Directories:

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