phyloPng Interactive Phylogenetic Tree Png Maker |
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Notes
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1. Length-ruler and length-values cannot be shown unless use-branch-lengths is also checked.
2. If "Strip underscore-suffixes?" is checked, underscores and anything following them are stripped from node labels.
3. For backwards compatibility, options exist to convert a dash or underscore to a space in a node label.
4. The tree is in the phastCons or .nh format name:length. Parentheses create a parent.
Parents must have two children. Length is not required if use-branch-lengths is not checked.
The length of the root branch is usually not specified.
Examples:
((A:0.1,B:0.1):0.2,C:0.15);
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:0.2,C:0.15);)
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((A:0.1,B:0.1)D:0.2,C:0.15)E;
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D:0.2,C:0.15)E;)
(internal or ancestral node labels)
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((((
(
((mouse,rat),human),
(dog,cow)
),
opossum),
chicken),
xenopus),
(tetraodon,zebrafish));
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,human),(dog,cow)),opossum),chicken),xenopus),(tetraodon,zebrafish));)
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We have extended the Newick format to allow spaces
and other non-alphanumeric characters in node labels.
If you need a backslash, comma, semi-colon, colon, or parenthesis,
it must be escaped with a back-slash character.
((Brandt's myotis \(bat\):0.1,
White-tailed eagle:0.1):0.2,
S. purpuratus:0.15);
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:0.1,White-tailed eagle:0.1):0.2,S. purpuratus:0.15);)
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5. PhastCons branch lengths are expected substitutions per site, allowing for
multiple hits. So a branch length of 0.5 means an average of one
substitution every two nucleotide sites, but the percent id will be
less than 50% because some of those substitutions are obscured by
subsequent substitutions. They are estimated from neutral sites,
sometimes fourfold degenerate sites in coding regions, or sometimes
"nonconserved" sites according to phastCons. The numbers are significant
to two or three figures.
6. Wrap-in-html is useful when the browser automatically shrinks a large image.
This option keeps the image view full in the browser automatically.
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