Core Orthologs

A Cnidaria-specific core single-copy ortholog resource (CCO), built from the same 153-proteome OrthoFinder run that powers the gene-family pages, with the species × orthogroup presence/absence matrix released alongside it. Where BUSCO scores a genome against a curated lineage, this defines the core on CnidoSite's own taxonomic sampling and lets you re-threshold it.

224core orthogroups 14strict tier 1,017extended tier 60genomes at ≥90% BUSCO 153proteomes scored 136,050member genes
Overview Core orthogroups Presence / copy number Species Download Methods

Download

Everything below is plain text or FASTA. The matrices are tab-separated with one row per genome. The first five columns are abbr1, latin, phylum, class and busco90 (the ≥90% BUSCO flag — not the site's stricter busco_summary.high_quality, see Methods); the remaining columns are one per core orthogroup, in the same order as the orthogroup column of core_og.tsv.

Matrices and tables

Presence / absence matrix 1/0 for all 153 proteomes × all 1,017 core orthogroups. TSV, gzipped. Copy-number matrix The same grid with the actual copy number (0, 1, 2, ...) instead of a flag. Single-copy matrix 1 exactly where the orthogroup is single-copy — ready to gate a concatenation. Core orthogroup table Per orthogroup: occupancy in five species sets, tier flags, outgroup coverage, best annotation. Core orthogroup members Long format — one row per orthogroup × genome × gene, with copy number. The matrix above, unpivoted. All 300,793 orthogroup scores The unfiltered score table. Re-threshold to any cutoff you like. Species table Taxonomy, BUSCO cnidaria_odb12 completeness, high-quality flag, CCO coverage.

Sequences

Core ortholog sequences Every member of every core orthogroup, unaligned. Headers are >CODE|gene OG_ID — the orthogroup is the second whitespace-delimited token, not part of the pipe-delimited ID. Supermatrix — strict Concatenated alignment plus strict.partitions.txt (AA, OG = start-end), in one archive. Supermatrix — core Concatenated alignment plus core.partitions.txt, in one archive. Supermatrix — extended Concatenated alignment plus extended.partitions.txt, in one archive. 43 MB uncompressed.
SupermatrixGenomes PartitionsColumns
strict 135 14 3,408
core 130 224 66,357
extended 144 1,017 367,759
The supermatrices reuse OrthoFinder's MAFFT alignments, subset to one sequence per genome per orthogroup, with columns kept only where at least half the partition's taxa have a residue, and sequences dropped below half the orthogroup's median length. They are starting points, not finished matrices: for a published tree, trim them further and pick a substitution model.
The gene sets are nested; the genome sets are not. Strict ⊂ core ⊂ extended holds for the orthogroups, so every gene in strict is also in core. It does not hold for the genomes, which is why the table above is not monotonic in either direction. Each tier admits a genome that is represented in at least half of that tier's partitions, and the strict tier only has 14 partitions to be represented in — so a genome can clear strict and miss core. Pick a tier for its gene set, and read the table to see which genomes come with it.

Sanity-check trees

The unrooted FastTree (-nosupport) trees referred to under Methods, so the monophyly claims there can be checked directly. No branch support, no model selection, no trimming — these are usability evidence, not a phylogeny.

strict.tree Newick, Strict tier, one line.core.tree Newick, Core tier, one line.extended.tree Newick, Extended tier, one line.
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