phyloGif Interactive Phylogenetic Tree Gif Maker
Use branch lengths?
  Show length ruler?
  Show length values?
  How many decimal places?
  Multiply branch length by factor?
Strip underscore-suffixes?
Change dash to space?
Change underscore to space?
Wrap in html page?
Monospace font?


  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.


(internal or ancestral node labels)
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);
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.