| [4212] | 1 | <HTML> |
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| 2 | <HEAD> |
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| 3 | <TITLE> "Newick's 8:45" Tree Format Standard </TITLE> |
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| 4 | </HEAD> |
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| 5 | <BODY> |
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| 6 | <PRE> |
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| 7 | Thursday, August 30, 1990 |
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| 8 | |
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| 9 | |
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| 10 | Gary Olsen's Interpretation of the "Newick's 8:45" Tree Format Standard |
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| 11 | |
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| 12 | (<A HREF=http://www.newicks.com>Here is the reason for the Newick name</A>) |
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| 13 | |
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| 14 | Conventions: |
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| 15 | Items in { } may appear zero or more times. |
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| 16 | Items in [ ] are optional, they may appear once or not at all. |
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| 17 | All other punctuation marks (colon, semicolon, parentheses, comma and |
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| 18 | single quote) are required parts of the format. |
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| 19 | |
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| 20 | |
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| 21 | tree ==> descendant_list [ root_label ] [ : branch_length ] ; |
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| 22 | |
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| 23 | descendant_list ==> ( subtree { , subtree } ) |
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| 24 | |
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| 25 | subtree ==> descendant_list [internal_node_label] [: branch_length] |
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| 26 | ==> leaf_label [: branch_length] |
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| 27 | |
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| 28 | root_label ==> label |
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| 29 | internal_node_label ==> label |
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| 30 | leaf_label ==> label |
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| 31 | |
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| 32 | label ==> unquoted_label |
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| 33 | ==> quoted_label |
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| 34 | |
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| 35 | unquoted_label ==> string_of_printing_characters |
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| 36 | quoted_label ==> ' string_of_printing_characters ' |
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| 37 | |
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| 38 | branch_length ==> signed_number |
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| 39 | ==> unsigned_number |
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| 40 | |
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| 41 | |
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| 42 | Notes: |
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| 43 | Unquoted labels may not contain blanks, parentheses, square brackets, |
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| 44 | single_quotes, colons, semicolons, or commas. |
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| 45 | Underscore characters in unquoted labels are converted to blanks. |
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| 46 | Single quote characters in a quoted label are represented by two single |
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| 47 | quotes. |
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| 48 | Blanks or tabs may appear anywhere except within unquoted labels or |
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| 49 | branch_lengths. |
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| 50 | Newlines may appear anywhere except within labels or branch_lengths. |
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| 51 | Comments are enclosed in square brackets and may appear anywhere |
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| 52 | newlines are permitted. |
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| 53 | |
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| 54 | |
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| 55 | Other notes: |
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| 56 | PAUP (David Swofford) allows nesting of comments. |
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| 57 | TreeAlign (Jotun Hein) writes a root node branch length (with a value of |
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| 58 | 0.0). |
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| 59 | PHYLIP (Joseph Felsenstein) requires that an unrooted tree begin with a |
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| 60 | trifurcation; it will not "uproot" a rooted tree. |
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| 61 | |
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| 62 | |
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| 63 | Example: |
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| 64 | |
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| 65 | (((One:0.2,Two:0.3):0.3,(Three:0.5,Four:0.3):0.2):0.3,Five:0.7):0.0; |
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| 66 | |
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| 67 | +-+ One |
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| 68 | +--+ |
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| 69 | | +--+ Two |
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| 70 | +--+ |
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| 71 | | | +----+ Three |
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| 72 | | +--+ |
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| 73 | | +--+ Four |
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| 74 | + |
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| 75 | +------+ Five |
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| 76 | |
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| 77 | </PRE> |
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| 78 | </BODY> |
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| 79 | </HTML> |
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