Table 2.

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

Item	Description	Typically included in tree files	Use by Open Tree of Life
Topology	The topology itself, plus the type of tree (e.g., gene tree vs. species tree, type of consensus tree)	Topology, but not tree type	Yes, topology; tree type used by curators as criteria to rank trees
Root	Whether the tree is rooted, and the location of the root	Tree in file often rooted arbitrarily; different from in manuscript figures	Yes, requires manual checking by curator to match against manuscript
OTU labels	Labels on tips of tree should include (or be mappable to) a meaningful online identifier	Yes, but often do not map to online databases	Tip labels mapped through combination of automated and manual processes
Branch lengths	The length of each branch of the tree, and the units of measurement	Branch length sometimes included; units generally not present	Imported into database when present, but not included on synthetic tree
Branch support	Support values (e.g., bootstrap proportions or Bayesian posterior probabilities)	Often in files, but support type often not specified	Not in algorithm, but curators do examine branch support
Character matrix	The 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 metadata	Number and type of genes used by curators as criteria to rank trees
Alignment method	Method used to align sequence data	No	No
Inference method	Method used to infer tree from data	Usually no	Inference 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.