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"

本数据集文件夹包含以下内容：
1. 直系同源组（Orthogroup）分配文件：经压缩的制表符分隔式电子表格，收录由OrthoFinder生成的直系同源组分配结果。
2. 花青素生物合成通路（Anthocyanin Biosynthetic Pathway, ABP）直系同源组校正文件包：经压缩的文件夹，内含花青素生物合成通路参考基因所在直系同源组的多序列比对结果、基因树以及基因树校正结果。此外还包含使用ASTRAL以Newick格式生成的物种树。
各文件后缀规范如下：
- 多序列比对文件：后缀为`.fa`
- 清洗后多序列比对文件：后缀为`.fa.cln`
- 扩展多数法则共识树：后缀为`.contree`
- 带根且经校正的基因树：后缀为`.recon`
- IQ-TREE日志文件：后缀为`.log`

3. 补充材料结果文件包：经压缩的文件夹，内含在线补充材料中描述的相关信息，具体包含：
(1) 制表符分隔式电子表格，收录与花青素生物合成通路参考基因的双向最佳比对同源基因结果；
(2) 由SonicParanoid鉴定得到的所有成对直系同源基因；
(3) OneKP数据集分析结果，包括花青素生物合成通路参考基因所在直系同源组的多序列比对结果、基因树以及基因树校正结果。此外还包含用于校正基因树的OneKP旗舰论文中所使用的主ASTRAL物种树。
各文件后缀规范如下：
- 多序列比对文件：后缀为`.fa`
- 清洗后多序列比对文件：后缀为`.fa.cln`
- 最大似然法进化树：后缀为`.tree`
- 经校正的基因树：后缀为`.recon`