Newick format offers a way of representing binary trees in text form by using
parentheses and commas. Here's an example of a straightforward rooted tree.
According to this tree, taxaa and b appear to be closely related, as do c and d.
More formally, a and b are said to be neighbors since they are adjacent to the
same internal node of the tree. We label this internal node using the syntax (a,b),
then delete a and b and iterate the process. In the end, the above tree can be represented
using Newick format as ((a,b),(c,d)).
The above rooted tree, which is more complex, can be represented by the following steps:
consolidate a and c into (a,c);
consolidate (a,c) and b into ((a,c),b);
consolidate d and e into (d,e);
consolidate f and g into (f,g);
consolidate (d,e) and (f,g) into ((d,e),(f,g));
consolidate the final two leaf nodes, ((a,c),b) and ((d,e),(f,g)), into the tree's final Newick representation
(((a,c),b),((d,e),(f,g))).
For unrooted trees, we may arbitrarily construct a root on any one of the tree's edges.
root picked arbitrarily at one of the internal edges. As a result, we will wind up with
different possible Newick formats. For example, the tree above tree can be
represented as (((a,b),c),(d,e)) or ((a,b),(c,(d,e))); try to find another representation of it.