((Human:0.3, Chimpanzee:0.2):0.1, Gorilla:0.3, (Mouse:0.6, Rat:0.5):0.2);
この方式は完全には標準化されていませんが、実質的には多くの解析プログラムで使われています。この方式の詳細は、Dr. Joe Felsenstein らによる PHYLIP (ver. 3.572) に付属の書類（main.doc）で説明されています。以下の文章は、そこからの引用です。
（引用ここから）
The Tree File
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In output from most programs, a representation of the tree is also written
into the tree file (usually named "treefile"). The tree is specified by the
nested pairs of parentheses, enclosing names and separated by commas. If there
are any blanks in the names, these must be replaced by the underscore character
"_". Trailing blanks in the name may be omitted. The pattern of the
parentheses indicates the pattern of the tree by having each pair of
parentheses enclose all the members of a monophyletic group. The tree file for
the above tree would have its first line look like this:
((Mouse,Bovine),((Orang,(Gorilla,(Chimp,Human))),Gibbon));
In the above tree the first fork separates the lineage leading to Mouse and
Bovine from the lineage leading to the rest. Within the latter group there is
a fork separating Gibbon from the rest, and so on. The entire tree is enclosed
in an outermost pair of parentheses. The tree ends with a semicolon. In some
programs such as DNAML, FITCH, and CONTML, the tree will be completely unrooted
and specified by a bottommost fork with a three-way split, with three
"monophyletic" groups separated by two commas:
(A,(B,(C,D)),(E,F));
The three "monophyletic" groups here are A, (B,C,D), and (E,F). The single
three-way split corresponds to one of the interior nodes of the unrooted tree
(it can be any interior node). The remaining forks are encountered as you move
out from that first node, and each then appears as a two-way split. You should
check the documentation files for the particular programs you are using to see
in which of these forms you can expect the user tree to be in. Note that many
of the programs that estimate an unrooted tree produce trees in the treefile in
rooted form! This is done for reasons of arbitrary internal bookkeeping. The
placement of the root is arbitrary.
For programs estimating branch lengths, these are given in the trees in
the tree file as real numbers following a colon, and placed immediately after
the group descended from that branch. Here is a typical tree with branch
lengths:
((cat:47.14069,(weasel:18.87953,((dog:25.46154,(raccoon:19.19959,
bear:6.80041):0.84600):3.87382,(sea_lion:11.99700,
seal:12.00300):7.52973):2.09461):20.59201):25.0,monkey:75.85931);
Note that the tree may continue to a new line at any time except in the middle
of a name or the middle of a branch length, although in trees written to the
tree file this will only be done after a comma.
These representations of trees are a subset of the standard adopted on
June 24, 1986 at the annual meetings of the Society for the Study of Evolution
at an meeting (the final session in Newick's lobster restaurant -- hence its
name -- the Newick standard) of an informal committee consisting of Wayne
Maddison (MacClade), David Swofford (PAUP), F. James Rohlf (NTSYS-PC), Chris
Meacham (COMPROB and plotting programs), James Archie (character coding
program), William H.E. Day, and me. This standard is a generalization of
PHYLIP's format, itself based on a well-known representation of trees in terms
of parenthesis patterns which has been around for almost a century. The
standard is now employed by most phylogeny computer programs but unfortunately
has yet to be decribed in a formal published description.