Data and scripts for: Nuclear phylogenomics clarifies the family-level backbone and gene-tree conflict in Zingiberales

This dataset contains the alignments, tree files, dating outputs, gene-tree conflict summaries, HyDe result matrices, scripts, tables, and figure files associated with a nuclear phylogenomic study of Zingiberales. The dataset includes 52 samples representing all eight families of Zingiberales and Pontederia crassipes as outgroup, 1566 low-copy nuclear CDS alignments, and a concatenated matrix of 1,868,754 aligned nucleotide sites. It also includes RAxML concatenated and single-gene trees, ASTRAL species trees inferred from the full and filtered gene-tree sets, treePL dating outputs, node-level gene-tree conflict summaries, empirical and simulated HyDe matrices, and files used to generate the main and supplementary figures. The archive is organized into directories for metadata, alignments, phylogenetic trees, divergence-time estimation, gene-tree conflict analyses, HyDe analyses, figures, and checksums. Sample accessions and source information are provided in the metadata tables.