Online Data for “Phylogenomics reveals convergent evolution of red-violet coloration in land plants and the origins of the anthocyanin biosynthetic pathway”

A folder containing the following items: Orthogroup Assignments A compressed tab-delimited spreadsheet containing orthogroup assignments from OrthoFinder. Anthocyanin Biosynthetic Pathway (ABP) Orthogroup Reconciliations A compressed folder containing the multiple sequence alignments, gene trees, and gene tree reconciliations for orthogroups containing reference genes in the anthocyanin biosynthetic pathway. Also included is the species tree generated using ASTRAL in Newick format. File endings: Multiple sequence alignment = ".fa" Cleaned multiple sequence alignment = ".fa.cln" Extended majority-rule consensus tree = ".contree" Rooted and reconciled gene tree = ".recon" IQ-TREE log file = ".log Supplementary Material Results A compressed folder containing information described in the Supplementary Material online. The following data are contained: (1) A tab-delimited spreadsheet containing the reciprocal best hits to reference genes in the anthocyanin biosynthetic pathway (2) All pairwise orthologs identified by SonicParanoid (3) The results from analysis of the OneKP dataset including multiple sequence alignments, gene trees, and gene tree reconciliations for orthogroups containing reference genes in the anthocyanin biosynthetic pathway. Also included is the main ASTRAL species tree from the OneKP capstone paper used to reconcile the gene trees. File endings: Multiple sequence alignment = ".fa" Cleaned multiple sequence alignment = ".fa.cln" Maximum likelihood tree = ".tree" Reconciled gene tree = ".recon"