Phylogenomic matrices, tree files, analysis scripts, and result tables for Delphinieae transcriptome phylogenomics

This dataset contains the reproducible phylogenomic analysis materials associated with the manuscript "Deep phylogeny, ancestral whole-genome duplication, and the evolution of bilaterally symmetrical flowers in Delphinieae".The deposited files include the final concatenated nuclear transcriptome alignment matrix, gene-tree and species-tree files, TreeShrink outputs, selected ortholog tables, whole-genome duplication result tables, gene-tree/species-tree conflict and hybridization-analysis scripts, configuration files, logs, and package-level audit metadata.Raw transcriptome sequencing reads generated for the study are not included in this Zenodo package because they have been deposited in the NCBI Sequence Read Archive. Sample-level SRA/DRA accession numbers are provided in Supplementary Table 1 of the manuscript. Large intermediate products, including raw/trimmed reads, transcriptome assemblies, CD-HIT/TransDecoder intermediate folders, bulky ProteinOrtho graph files, and sampled-position replicate directories, were intentionally excluded to keep the repository package focused on reusable and reproducible analysis materials. The file mpe_excluded_large_or_raw.tsv documents the main excluded large files.