Reuman Lab · mammal phylogenetics

Dated mammal phylogenies,
served as a database.

10,000 draws over 9,507 species, in four anchor × coverage variants — decomposed into an indexed columnar store. Sample draws, prune to a clade, get posterior divergence ages and per-order consensus trees.

10,000draws / set
9,507species
201.45Ma root (LSD2)
4anchors × coverage
posterior draws · Macroscelidea

01 The sets

Two coverages — DNA-sampled (dna, 7,901 tips) and MDD-completed (comp, 9,507 tips) — each dated under two anchors. Draw index i is the same underlying draw across all four.

02 Explorer

Pull a sample of posterior draws, pruned to a group — rendered live from the columnar store. Then take the same sample home as Newick.

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03 Consensus

Consensus per mammal order — majority-rule, extended majority-rule, or the maximum-clade-credibility draw — over a translucent sample of the posterior.

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04 Divergence lab

The posterior distribution of a divergence time is the whole point of a credible set. Pick two species; get the MRCA age in every draw.

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05 Data

The release verbatim: gzipped multi-Newick (one tree per line, line = draw index), MCC summaries, draw manifests, validation tables. Integrity via md5sum -c md5sums.txt.

Format, correspondence and caveats: release README.

06 API

Everything the site does is a public endpoint. Newick out, JSON or plain text.

GET /api/setsset metadata
GET /api/tree/{set}/{idx}?tax=mdd|gbif|iucnone draw, verbatim with taxonomy projection
GET /api/sample/{set}?n&seed&tax=random draws, multi-Newick
GET /api/prune?tree_set&ord|family|genus|tips&n&seed&tax=draws pruned to group under taxonomy view
GET /api/ages?tree_set&tips&nMRCA-age posterior (source tip labels)
GET /api/clades/{set}?min_freqposterior clade support
GET /api/consensus/{set}/{ord}?kind=mr|emr|mcc&tax=per-order consensus with taxonomy projection
GET /api/order_clades/{set}/{ord}restricted splits + ages
GET /api/tips?q&ord&family&genustaxon search (returns stable psid)
GET /api/download/{path}release files