String representation of a tree

All trees used by the programs follow the newick standard though the grammar in PHASE is more limited. The newick format uses the recursive definition of a tree to represent phylogenies in a computer readable form with nested parentheses. The tree in figure 2.1 can be written:

$$(Outgroup,gorilla,(human,chimpanzee));$$

However one must be aware that this representation is not unique, the following one works as well:

$$(human,(Outgroup,gorilla),chimpanzee));$$

Sometimes, when an outgroup was provided, the rooted representation is used in PHASE:

$$(Outgroup,(gorilla,(human,chimpanzee)))$$