NewickFormat < Main

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---++ NewickFormat

"Newick" or "New Hampshire" format is a string representation of a phylogenetic tree using nested parentheses.
It's exported by all major phylogenetic software including PHYLIP, PAML, DART and many more.

The format is described, with some napkin-science [[http://www.newicks.com/][history]], on the [[http://evolution.genetics.washington.edu/phylip/newicktree.html][<nop>PHYLIP section of Joe Felsenstein's washington.edu]] site.

Here is the grammar for Newick format (from [[http://evolution.genetics.washington.edu/phylip/newick_doc.html][Gary Olsen]]):


<pre>
Conventions:
   Items in { } may appear zero or more times.
   Items in [ ] are optional, they may appear once or not at all.
   All other punctuation marks (colon, semicolon, parentheses, comma and
         single quote) are required parts of the format.


              tree ==> descendant_list [ root_label ] [ : branch_length ] ;

   descendant_list ==> ( subtree { , subtree } )

           subtree ==> descendant_list [internal_node_label] [: branch_length]
                   ==> leaf_label [: branch_length]

            root_label ==> label
   internal_node_label ==> label
            leaf_label ==> label

                 label ==> unquoted_label
                       ==> quoted_label

        unquoted_label ==> string_of_printing_characters
          quoted_label ==> ' string_of_printing_characters '

         branch_length ==> signed_number
                       ==> unsigned_number


Notes:
   Unquoted labels may not contain blanks, parentheses, square brackets,
        single_quotes, colons, semicolons, or commas.
   Underscore characters in unquoted labels are converted to blanks.
   Single quote characters in a quoted label are represented by two single
        quotes.
   Blanks or tabs may appear anywhere except within unquoted labels or
        branch_lengths.
   Newlines may appear anywhere except within labels or branch_lengths.
   Comments are enclosed in square brackets and may appear anywhere
        newlines are permitted.


Other notes:
   PAUP (David Swofford) allows nesting of comments.
   TreeAlign (Jotun Hein) writes a root node branch length (with a value of
        0.0).
   PHYLIP (Joseph Felsenstein) requires that an unrooted tree begin with a
        trifurcation; it will not "uproot" a rooted tree.


Example:

   (((One:0.2,Two:0.3):0.3,(Three:0.5,Four:0.3):0.2):0.3,Five:0.7):0.0;

           +-+ One
        +--+
        |  +--+ Two
     +--+
     |  | +----+ Three
     |  +-+
     |    +--+ Four
     +
     +------+ Five

</pre>

-- Biowiki page created by AlexCoventry - 28 Feb 2005
Topic revision: r16 - 2007-12-03 - IanHolmes