Ed's Big Plans

Brief: The Newick format offers a nice flat representation of a tree. This is done by performing a depth-first (prefix) traversal on the tree and documenting each of the nodes and lengths of edges as they occur during that traversal. Note that this representation is only valid for directed acyclic graphs and inherently preserves the parent-child relationships between the nodes. While there is no restriction on where a root node is for a particular set of data, the format indirectly specifies a root node as the last node to be visited in the traversal. The Newick format is used in phylogenetic trees, and is inherited by MUSCLE through compatibility with PHYLIP. The format does not state a particular arity, although the culture of phylogenetics has made the binary tree the most common flavour. Finally, due to the regular nature of its encoding, Newick format strings are just as regular to convert back to their in-memory representations.