University of Glasgow

Roderic Page

It\'s Friday, so time for some random, half-baked ideas. Imagine that we
have a database of evolutionary trees, and these overlap for a set of
taxa that we are interested in. How do we summarise these trees? One
approach is to make a supertree. It would be useful to display the
subtrees that went into making this supertree, if only to give an idea
of how much they agree with the supertree. How to do this?  
  
One idea I\'ve been toying with is inspired by
[Photosynth](http://photosynth.net/), from Microsoft labs (it only runs
on Windows, sigh). Photosynth takes a series of pictures taken from
different angles and stiches them together into a 3D model of the object
being photographed:  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhxWLOJPdq1LhnlXbHjzyEPnEw5OZmemgREQoLN_mSb2Ly70pZRTAFTH_YeC9b-aBItaFqFIpB8ZQ0Jph1HfZUoep88I5ExnccodaWz2h_odui7QchiFxNp5JR1Zpw4U3DS2LnG/s400/photosynth.jpg){#BLOGGER_PHOTO_ID_5310027871757899586
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 305px;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhxWLOJPdq1LhnlXbHjzyEPnEw5OZmemgREQoLN_mSb2Ly70pZRTAFTH_YeC9b-aBItaFqFIpB8ZQ0Jph1HfZUoep88I5ExnccodaWz2h_odui7QchiFxNp5JR1Zpw4U3DS2LnG/s1600-h/photosynth.jpg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
  
One thing I like about Photosynth is that you can see the original
pictures, so when you move around the view you get a sense of how they
have contributed to the overall view. This is easier to see than
explain:  
  

  
  
Now, imagine if we did this with trees. We could create a supertree as a
summary of the individual trees, then have the original trees layered on
top. Perhaps we could do this in 3D, so that each individual tree is in
a plane that is tilted with respect to the supertree in proportion to
how much it disagrees with the supertree:  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiPUmF4U1QCR9blIBLdefVl1byxQ5teQHB3zVEtwZyE6doK5BM_XZ4kKHrFe2AKuOVx01YSlrXZDzDdGDZ4p5ihN3ppcT4Bb6xoIzq185nnwAyM_DtTUJ5A3ZNshpH6BSoipExi/s400/phototree.jpg){#BLOGGER_PHOTO_ID_5310032549276503842
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 352px; height: 154px;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiPUmF4U1QCR9blIBLdefVl1byxQ5teQHB3zVEtwZyE6doK5BM_XZ4kKHrFe2AKuOVx01YSlrXZDzDdGDZ4p5ihN3ppcT4Bb6xoIzq185nnwAyM_DtTUJ5A3ZNshpH6BSoipExi/s1600-h/phototree.jpg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
I think this could be a fun way to explore a set of trees, and it would
give one the ability to quickly grasp how well the source trees agreed
with the supertree. Note that I\'m not (necessarily) arguing that the
supertree represents the try phylogeny. Think of it as a convenient way
to summarise the individual trees.  
  
Part of what attracts me to this approach is that I think most, if not
all, 3D phylogeny viewers (such as
[Paloverde](http://loco.biosci.arizona.edu/paloverde/paloverde.html) and
the [Wellcome tree of
life](http://iphylo.blogspot.com/2009/02/thoughts-on-wellcome-interactive-tree.html))
don\'t make any real use of 3D, beyond the rather gimmicky (and I find
ultimately confusing) ability to fly around a 2D tree. Is there a better
way to exploit the possibilities of 3D?


It's Friday, so time for some random, half-baked ideas. Imagine that we have a database of evolutionary trees, and these overlap for a set of taxa that we are interested in. How do we summarise these trees? One approach is to make a supertree. It would be useful to display the subtrees that went into making this supertree, if only to give an idea of how much they agree with the supertree.

Rogue Scholar Beiträge

Photosynth for trees - supertrees revisited