phylogenetic tree layout or PhyloTree update

[mousem...@gmail.com]

I am interested in having Cytoscape display phylogenetic trees in their standard formats (e.g. rectangular, circular or angled/slanted phylogram/cladogram, like here). I see that there is a PhyloTree plugin that worked with versions up to Cytoscape 2.8 to at least create angular format trees. It don't see any evidence of work toward the plugin being updated to a Cytoscape 3 app. Is there a way to get Cytoscape 3 to display a rectangular phylogenetic tree?

-- Eric

[Scooter Morris]

Hi Eric,
   The short answer is "no", unfortunately.  If there is enough of a desire, we could port the phylotree plugin, to Cytoscape 3, however.  It was originally a Google Summer of Code project and we still have the original code.   Do you think there would be others who might be interested?

-- scooter

[mousem...@gmail.com]

Thank you for the reply, scooter. I don't know for certain if there are others who would be interested in an updated Phylotree plugin, but the other options for phylogenetic tree display right now are limited. There are development groups around Archaeopteryx and TreeGraph but I am finding that both struggle with consistent annotation support in their import/export file abilities. Import/export file compatibility is hard in part because there are competing new standards in the phylogenetic tree space for a modern XML phylogeny file format (neXML and phyloXML), and none of the phylogenetic tree software works with Cytoscape's GML or XGMML file standards.

Cytoscape is more advanced and appears to be more actively under development than the other options, so it would be very good to be able to tie together these projects with a compatibility plugin that also would allow Cytoscape display in the usual phylogram/cladogram tree formats. I suppose if anyone else finds and responds to this message thread then we'll learn if there is other interest. :-)

-- Eric

[Barry Demchak]

Hi, Eric –

 

FYI, here is the repository … https://github.com/nrnb/gsoc2009chinmoy

 

I think this may make a good demonstration service for the Cytoscape Cyberinfrastructure.

 

Instead of delivering it as a monolithic app, we could deliver it as an app + a REST-callable service. That way, Cytoscape users *and* R/Python users could use it, too.

 

We would get the benefit of demonstrating a Java algorithm being exposed as a CI service.

 

Sound interesting?

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