Table 2.

Tree metadata, based on the MIAPA checklist (https://github.com/miapa/miapa)

ItemDescriptionTypically included in tree filesUse by Open Tree of Life
TopologyThe topology itself, plus the type of tree (e.g., gene tree vs. species tree, type of consensus tree)Topology, but not tree typeYes, topology; tree type used by curators as criteria to rank trees
RootWhether the tree is rooted, and the location of the rootTree in file often rooted arbitrarily; different from in manuscript figuresYes, requires manual checking by curator to match against manuscript
OTU labelsLabels on tips of tree should include (or be mappable to) a meaningful online identifierYes, but often do not map to online databasesTip labels mapped through combination of automated and manual processes
Branch lengthsThe length of each branch of the tree, and the units of measurementBranch length sometimes included; units generally not presentImported into database when present, but not included on synthetic tree
Branch supportSupport values (e.g., bootstrap proportions or Bayesian posterior probabilities)Often in files, but support type often not specifiedNot in algorithm, but curators do examine branch support
Character matrixThe data used to infer the tree, including data type and source (e.g., GenBank accession or specimen)Sometimes included with tree file, but often without sufficient metadataNumber and type of genes used by curators as criteria to rank trees
Alignment methodMethod used to align sequence dataNoNo
Inference methodMethod used to infer tree from dataUsually noInference method used by curators as criteria to rank trees
  • We note whether the metadata is generally available in the tree file (as opposed to in the text of the article, if at all) and how the data are used by Open Tree of Life.