package Parsimony

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Used in: data

• string node_name = 1

  The node name as given in the newick tree

• repeated string condensed_leaves = 2

  A list of strings for the names of identical sequences all of which are represented by the node above

• string newick = 1

  Newick tree string. May contain distances, but note that these may be distinct from distances as calculated with UShER

• repeated mutation_list node_mutations = 2

  Mutations_list object for each node of this tree, in the order that nodes are encountered in a preorder traversal of the tree in the newick string

• repeated condensed_node condensed_nodes = 3

  A dictionary-like object mapping names in the newick tree to a larger set of identical nodes that have been collapsed into this single node

• repeated node_metadata metadata = 4

  Clade annotations on a per-node basis, in the order that nodes are encountered in a preorder traversal of the tree

Used in: mutation_list

• int32 position = 1

  Position in the chromosome

• int32 ref_nuc = 2

  All nucleotides are encoded as integers (0:A, 1:C, 2:G, 3:T)

  Reference nucleotide at this position

• int32 par_nuc = 3

  Nucleotide of parent at this position

• repeated int32 mut_nuc = 4

  Mutated nucleotide in this node at this position

• string chromosome = 5

  Chromosome string. Currently unused.

Used in: data

• repeated mut mutation = 1

Used in: data

• repeated string clade_annotations = 1