ELF-NET Data S4: RuBisCO lineage analysis package

ELF-NET Data S4: RuBisCO lineage analysis (consolidated v2.0 — supersedes Data S4a/S4b/S4c).

This package contains every artifact required to reproduce the lineage-resolved RuBisCO analyses in the manuscript: (1) Form I (chloroplast) per-sample hmmsearch counts for 2,372 samples, stratified by 15 lineage-specific HMM profiles; (2) Form II (nuclear) per-sample hmmsearch counts using a curated Form II HMM; and (3) the HMM profile library and reference alignments, plus raw/filtered/non-redundant input sequences used to build each HMM.

Structure:

• DataS4_rubisco_lineage_package/README.md — top-level package README
• form_I_chloroplast/ — 2,372 per-sample Form I count TSVs (formerly Data S4a, 10.5281/zenodo.18786756)
• form_II_nuclear/ — 2,372 per-sample Form II count TSVs (formerly Data S4b, 10.5281/zenodo.18786759)
• hmm_profiles_and_alignments/ — 18 lineage HMMs, MAFFT alignments, CD-HIT-clustered input sequences (formerly Data S4c)
• SHA256SUMS.txt — SHA-256 hashes over every non-README file

Related to Figure 1 and STAR Methods — RuBisCO lineage analysis.

Superseded deposits (not deleted; still resolvable): Data S4a (10.5281/zenodo.18786756), Data S4b (10.5281/zenodo.18786759), and the prior v1 of this record (Data S4c, 10.5281/zenodo.18786775).