ChlORIS: Chloroplast Orthologs Resource & Identification Suite

ChlORIS (Chloroplast Orthologs Resource and Identification Suite) groups the plastid-encoded proteins of algal phyla into orthologous gene families for evolutionary and metagenomic research. Full description and interactive browsing at chloris.csic.es. All files are released under CC0 1.0, with one exception noted below. ChlORIS_core_msa_v1.0.tar.gz: multiple sequence alignments (aligned FASTA) for the 224 core plastid orthogroups shown in detail on the ChlORIS website. Headers formatted protein_id|gene_name. ChlORIS_msa_v1.0.tar.gz: multiple sequence alignments for the full set of 496 named plastid orthogroups. protein_msdb_v1.0.tar.gz: CheckM compatible metagenomic reference database: profile HMMs, lineage specific marker gene sets, and the curation tree needed to place a plastid MAG in the taxonomy. Built for use with ChloroScan. ChlORIS_hmms_v1.0.tar.gz: profile HMMs (HMMER3 format) for all 496 named orthogroups. The 224 core orthogroups include calibrated noise and trusted score cutoffs. ChlORIS_OGs_unknown_v1.0.tar.gz: orthogroups whose members are mainly hypothetical or uncharacterized ORFs, with non canonical identifiers. Pfam_Protein_Mapping_v1.0.tsv: HHsuite results giving the probability of 989 Pfam domains being present in 470 core proteins. Tab delimited. protein_cifs_v1.0.tar.gz: predicted structures (mmCIF) for the 224 core proteins, modelled with AlphaFold 3. Subject to the AlphaFold 3 Output Terms of Use, not CC0. ChlORIS_v1.0.contree: Newick tree with 865 leaves: 857 algal taxa, 1 land plant reference, and 7 cyanobacterial outgroups. Built from 51 conserved marker genes. galah_cluster_reps_filtered_v1.0.tsv: genome cluster representative table underlying the Species page: representative genome, member accessions, tree and MSA membership, taxonomy, and specimen identifiers. ChlORIS_core_cds_aln_v1.0.tar.gz: codon alignments (CDS nucleotides aligned to the protein alignment) for the 224 core plastid orthogroups. ChlORIS_cds_aln_v1.0.tar.gz: codon alignments for the full set of 496 named plastid orthogroups. ChlORIS_OGs_unknown_cds_aln_v1.0.tar.gz: codon alignments for the 2029 OGs_unknown orthogroups (mainly hypothetical or uncharacterized ORFs). ChlORIS_metadata_v1.0.tsv.gz: per-protein table (protein_id, genome_acc, species, taxonomy, representative genome) for every genome in the release, used by downstream tools to resolve taxa and genomes by name.