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<TITLE> "Newick's 8:45" Tree Format Standard </TITLE>
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<PRE>
Thursday, August 30, 1990
Gary Olsen's Interpretation of the "Newick's 8:45" Tree Format Standard
(<A HREF=http://www.newicks.com>Here is the reason for the Newick name</A>)
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
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