43 | | * '''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 |
44 | | * '''Pair of Trees''' - exactly two trees, which function as inputs for tree reconciliation (e.g. duplication inference) or for tree-to-tree distance calculations |
45 | | * '''Set of Trees''' - input for consensus calculations, or as query topologies |
46 | | * '''One OTU''' - exactly one OTU for which associated data (trees or matrices that contain it) and metadata might be retrieved |
47 | | * '''Pair of OTUs''' - exactly two OTUs, as input for topological queries (MRCA) and calculations (patristic distance) |
48 | | * '''Set of OTUs''' - input for topological queries (MRCA) and for which data (trees or matrices that contain them) and metadata might be retrieved |
49 | | * '''One Node''' - input for tree traversal operations (parent, children) and for which metadata might be retrieved |
50 | | * '''Pair of Nodes''' - input for topological queries (MRCA) and calculations (patristic distance) |
51 | | * '''Set of Nodes''' - input for topological queries (MRCA) |
52 | | * '''One Character''' - exactly one character (matrix column) for which calculations are performed (variability) and metadata is retrieved |
53 | | * '''Set of Characters''' - input as filter predicate, to retrieve OTUs that contain recorded states for the characters |
54 | | * '''One Character State Sequence''' - for which metadata is retrieved |
55 | | * '''Pair of Character State Sequences''' - as input for pairwise alignments, as input to calculate pairwise divergence |
56 | | * '''Set of Character State Sequences''' - as input for multiple sequence alignment |
57 | | * '''Character State Matrix''' - as input for inference (of one tree or set of trees), as input for calculations (average sequence divergence) and for which metadata is retrieved |
| 43 | * ''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 |
| 44 | * ''Pair of Trees'' - exactly two trees, which function as inputs for tree reconciliation (e.g. duplication inference) or for tree-to-tree distance calculations |
| 45 | * ''Set of Trees'' - input for consensus calculations, or as query topologies |
| 46 | * ''One OTU'' - exactly one OTU for which associated data (trees or matrices that contain it) and metadata might be retrieved |
| 47 | * ''Pair of OTUs'' - exactly two OTUs, as input for topological queries (MRCA) and calculations (patristic distance) |
| 48 | * ''Set of OTUs'' - input for topological queries (MRCA) and for which data (trees or matrices that contain them) and metadata might be retrieved |
| 49 | * ''One Node'' - input for tree traversal operations (parent, children) and for which metadata might be retrieved |
| 50 | * ''Pair of Nodes'' - input for topological queries (MRCA) and calculations (patristic distance) |
| 51 | * ''Set of Nodes'' - input for topological queries (MRCA) |
| 52 | * ''One Character'' - exactly one character (matrix column) for which calculations are performed (variability) and metadata is retrieved |
| 53 | * ''Set of Characters'' - input as filter predicate, to retrieve OTUs that contain recorded states for the characters |
| 54 | * ''One Character State Sequence'' - for which metadata is retrieved |
| 55 | * ''Pair of Character State Sequences'' - as input for pairwise alignments, as input to calculate pairwise divergence |
| 56 | * ''Set of Character State Sequences'' - as input for multiple sequence alignment |
| 57 | * ''Character State Matrix'' - as input for inference (of one tree or set of trees), as input for calculations (average sequence divergence) and for which metadata is retrieved |
60 | | * '''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) |
61 | | * '''Float''' - a floating point value, for topology metrics (balance, stemminess, resolution) tree-to-tree distances (symmetric difference), patristic distance, sequence divergence |
62 | | * '''String''' - for metadata, e.g. descriptions |
63 | | * '''Stringvector''' - for metadata, e.g. a set of tags |
| 60 | * ''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) |
| 61 | * ''Float'' - a floating point value, for topology metrics (balance, stemminess, resolution) tree-to-tree distances (symmetric difference), patristic distance, sequence divergence |
| 62 | * ''String'' - for metadata, e.g. descriptions |
| 63 | * ''Stringvector'' - for metadata, e.g. a set of tags |