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Table 3 Input and output data types relevant for phyloinformatic web services.
| Inputs - The input data types defined here do not imply pass-by-value, and could be passed as an identifier: | |
|---|---|
| One Tree | exactly one tree, which might function as a query topology, as an input for topology metric calculations, or as something for which associated data (matrices) and metadata might be retrieved |
| Pair of Trees | exactly two trees, for tree reconciliation (e.g. duplication inference) or for tree-to-tree distance calculations |
| Set of Trees | input for consensus calculations, or as query topologies |
| One OTU | exactly one OTU for which associated data (trees or matrices that contain it) and metadata might be retrieved |
| Pair of OTUs | exactly two OTUs, as input for topological queries (MRCA) and calculations (patristic distance) |
| Set of OTUs | input for topological queries (MRCA) and for trees or matrices that contain them, and metadata is retrieved |
| One Node | input for tree traversal operations (parent, children) and for which metadata might be retrieved |
| Pair of Nodes | input for topological queries (MRCA) and calculations (patristic distance) |
| Set of Nodes | input for topological queries (MRCA) |
| One Character | exactly one character (matrix column) for which calculations are performed (variability) and metadata is retrieved |
| Set of Characters | input as filter predicate, to retrieve OTUs that contain recorded states for the characters |
| One Character State Sequence | input for which metadata is retrieved |
| Pair of Character State Sequences | input for pairwise alignments, as input to calculate pairwise divergence |
| Set of Character State Sequences | input for multiple sequence alignment |
| Character State Matrix | input for inference (of one tree or set of trees), for calculations (average sequence divergence) and metadata retrieval |
| Outputs - In addition to the mirroring the inputs described above, some 'primitives' may be required: | |
| Int | an integer, for things such as topology metrics (node counts) tree-to-tree distances (in branch moves) node distances (in number of nodes in between), character state counts, sequence divergence (substitution counts, site counts) |
| Float | a floating point value, for topology metrics (balance, stemminess, resolution) tree-to-tree distances (symmetric difference), patristic distance, sequence divergence |
| String | for metadata, e.g. descriptions |
| Stringvector | for metadata, e.g. a set of tags |
