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phyloGif Interactive Phylogenetic Tree Gif Maker |
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1. Length-ruler and length-values cannot be shown unless use-branch-lengths is also checked.
2. Underscores and anything following them are automatically stripped from node labels
unless the preserve-underscores checkbox is checked, in which case they are converted to spaces.
3. If a space is required in a node label, enter it as a dash.
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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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 shinks a large image.
This option keeps the image view full in the browser automatically.
However, do not use with IE6 when performing save-as.
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