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One Tree
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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
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Pair of Trees
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exactly two trees, for tree reconciliation (e.g. duplication inference) or for tree-to-tree distance calculations
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Set of Trees
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input for consensus calculations, or as query topologies
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One OTU
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exactly one OTU for which associated data (trees or matrices that contain it) and metadata might be retrieved
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Pair of OTUs
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exactly two OTUs, as input for topological queries (MRCA) and calculations (patristic distance)
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Set of OTUs
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input for topological queries (MRCA) and for trees or matrices that contain them, and metadata is retrieved
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One Node
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input for tree traversal operations (parent, children) and for which metadata might be retrieved
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Pair of Nodes
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input for topological queries (MRCA) and calculations (patristic distance)
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Set of Nodes
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input for topological queries (MRCA)
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One Character
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exactly one character (matrix column) for which calculations are performed (variability) and metadata is retrieved
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Set of Characters
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input as filter predicate, to retrieve OTUs that contain recorded states for the characters
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One Character State Sequence
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input for which metadata is retrieved
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Pair of Character State Sequences
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input for pairwise alignments, as input to calculate pairwise divergence
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Set of Character State Sequences
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input for multiple sequence alignment
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Character State Matrix
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input for inference (of one tree or set of trees), for calculations (average sequence divergence) and metadata retrieval
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Outputs - In addition to the mirroring the inputs described above, some 'primitives' may be required:
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Int
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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)
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Float
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a floating point value, for topology metrics (balance, stemminess, resolution) tree-to-tree distances (symmetric difference), patristic distance, sequence divergence
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String
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for metadata, e.g. descriptions
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Stringvector
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for metadata, e.g. a set of tags
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