PhyloStyloTastic

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Phylostylotastic.png

Why PhyloStyloTastic?

Phylogenies are generally thought of as a stand-alone data structure with a topology, branch lengths, and names for the tips. However, when trees are used for illustrative purposes in publication or presentation, authors often modify and decorate the visualization of the tree to display data that is affiliated with particular branches, nodes, or the diagram overall, in order to convey extra meaning that is not encoded in the tree structure itself.

Currently, there is no standardized way for authors to share these marked-up trees with others outside of either graphics files or specialized tree viewing software. No existing tree visualization packages share a common notation for these modified files.

Sharing graphics files directly drastically limits the reusability of the marked-up trees: it is impossible to programatically communicate shared conventions for commonly-used notations, like branch support values, clade names, character states, etc. If the values for these markups change, the author must edit the graphic file manually, making versioning difficult.

As well, different authors, journals, and communities may have alternative preferred conventions for notating certain types of commonly used data. If a group of authors makes an editorial decision to denote e.g., high clade support values as a bolded branch, and another group decides to use asterisks to indicate the same data, the tree should be able to be interpreted by viewers and visualized using either style programatically and easily.

PhyloStyloTastic is a set of standards to address these problems.

Full .TSS spec

TODO:

  • Figure out how to extend nexml (ALL)
    • use <meta> tag with property as a css class (done)
  • Determine .TSS spec (ALL)
    • done, linked above
  • Document the spec formally (Mike)
    • in progress
  • Document the necessary interfaces to tree viewing packages
  • Make test extended nexml and .tss files to use on the tree viewers (Mike)
    • done
  • Get tree viewers (TopiaryExplorer, Mesquite) (Meg, Daisie)
    • read nexml (TE:in progress, M:done)
    • read .tss (TE:not started, M:in progress)
    • color things according to the .tss (TE:not started, M:done)

Example node <meta> definitions and their corresponding .tss style specs:

 //<meta property="tss:taxonomic_level" content="family">
 taxonomic_level.family {collapsed : true;}
 // to add more than one node label with special formatting:
 // <meta property="tss:labeled_clade" content="ruelliae">
 labeled_clade.ruelliae {
 	text : "Clade Ruelliae";
 	font-family : Helvetica;
 	font-size : 300%;
 	color: #00135F;
 	font-style : bold;
 }
 //<meta property="tss:trophic_level” content=”herbivore”>
 trophic_level.herbivore {
 	color : #00FF00;
 }
 //<meta property="tss:trophic_level” content=”herbivore”>
 trophic_level.herbivore {
 	color : #00FF00;
 	image : "./herbivore.png";
 }
 //<meta property="tss:trophic_level” content=”carnivore”>
 trophic_level.carnivore {
 	color : #ff0000;
 }