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Glossary

Newick format

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.

Example Tree 1

According to this tree, taxa a 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)).

Example Tree 2

The above rooted tree, which is more complex, can be represented by the following steps:

Example Tree 3

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.

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