Data and code for: An ancient gene programme shared by primary larvae across animal phyla

Processed data and code for the paper “An ancient gene programme shared by primary larvae across animal phyla”. The deposit contains (i) per-species orthogroup expression tables for larval and adult transcriptomes quantified from public RNA-seq runs, orthogroup gene counts, per-gene methylation tables, the species tree and the curated run labels, together with the analysis code that repeats every analysis of the paper (analysis/); (ii) the data and code of the analyses added in revision, with checksums of their outputs (revision_v4/); (iii) the metadata-curation scripts, the instructions given to language models and the record of every model call (curation/); and (iv) the scripts that produced the processed data from public sequencing reads (processing/). All raw sequencing data are public in ENA/SRA. See README.md.