University of Glasgow

Roderic Page

I\'ve made some progress on a [wiki of
phylogenies](http://iphylo.blogspot.com/2009/09/towards-wiki-of-phylogenies.html).
Still much to do, but here are some samples of what I\'m trying to do.  
  
First up, here\'s an example of a publication
<http://iphylo.org/treebase/Doi:10.1016/j.ympev.2008.02.021>:  

::: {style="text-align:center;"}
![wiki1.png](http://lh5.ggpht.com/_Gct8lVAxKqQ/S6AI2eevujI/AAAAAAAAAng/QlMt0a0NxII/wiki1.png?imgmax=800){border="0"
width="400" height="332"}
:::

  
In addition to basic bibiographic details we have links to GenBank
sequences and a phylogeny. The sequences are georeferenced, which
enables us to generate a map. At a glance we see that the study area is
central America.  
  
This study published the following
[tree](http://iphylo.org/treebase/Tree5692):  

::: {style="text-align:center;"}
![wiki2.png](http://lh6.ggpht.com/_Gct8lVAxKqQ/S6AKCLgVuPI/AAAAAAAAAno/9FbFnoJmQXU/wiki2.png?imgmax=800){border="0"
width="400" height="298"}
:::

  
The tree is displayed using my
[tvwidget](http://code.google.com/p/tvwidget/). A key task in
constructing the wiki is mapping labels used in TreeBASE to other
taxonomic names, for example, those in the NCBI taxonomy database. This
is something I first started working on in the
[TbMap](http://linnaeus.zoology.gla.ac.uk/~rpage/tbmap/) project
([doi:10.1186/1471-2105-8-158](http://dx.doi.org/10.1186/1471-2105-8-158)).
In the context of this wiki I\'m explicitly mapping TreeBASE taxa to
NCBI taxa. Taxa are modelled as \"namestrings\" (simple text strings),
OTUs (TreeBASE taxa), and taxonomic concepts (sets of observations or
taxa). For example, the [tree](http://iphylo.org/treebase/Tree5692)
shown above has numerous samples of the frog *Pristimantis ridens*, each
with a unique label (namestring) that includes, in this case, voucher
specimen information (e.g., \"Pristimantis ridens La Selva AJC0522
CR\"). Each of these labels is mapped to the NCBI taxon [*Pristimantis
ridens*](http://iphylo.org/treebase/Ncbi:228422).  
  
One thing I\'m interested in doing is annotating the tree. Eventually I
hope to generate (or make it easy to generate) things such as [Google
Earth
phylogenies](http://iphylo.blogspot.com/2007/06/google-earth-phylogenies.html)
(via georeferenced sequences and specimens). For now I\'m playing with
generating nicer labels for the terminal taxa. As it stands if you
download the original tree from TreeBASE you have the original
study-specific labels (e.g., \"Pristimantis ridens La Selva AJC0522
CR\"), whereas it would be nice to also have taxonomic names (for
example, if you wanted to combine the tree or data with another study).
Below the tree you\'ll see a NEXUS NOTES block with the \"ALTTAXNAMES\"
command. The program [Mesquite](http://mesquiteproject.org/) can use
this command to enable users to toggle between different labels, so that
you can have either a tree like this:  

::: {style="text-align:center;"}
![wiki3.png](http://lh4.ggpht.com/_Gct8lVAxKqQ/S6AQ4ZWGGhI/AAAAAAAAAnw/RzJSeJF1BAk/wiki3.png?imgmax=800){border="0"
width="400" height="295"}
:::

  
or a tree like this:  

::: {style="text-align:center;"}
![wiki4.png](http://lh5.ggpht.com/_Gct8lVAxKqQ/S6AQ9V6XhlI/AAAAAAAAAn0/lCcIp2h93aU/wiki4.png?imgmax=800){border="0"
width="380" height="337"}
:::


I've made some progress on a wiki of phylogenies. Still much to do, but here are some samples of what I'm trying to do.  First up, here's an example of a publication http://iphylo.org/treebase/Doi:10.1016/j.ympev.2008.02.021:    In addition to basic bibiographic details we have links to GenBank sequences and a phylogeny. The sequences are georeferenced, which enables us to generate a map.

Progress on a phylogeny wiki

[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFkSIx2BvhY8hZH68cBWWmsX4PxXCt2yp-XX-G1TXza6nUQ7UOVvPCfRmNtFhDgSqwU9LJWpuIuFa07AUHib9eF3vmRk7GdATnAMvX2t0wMewnbKBg6t2rf5oK6_Bi2hySbmPs/s320/Mesquite.jpg){#BLOGGER_PHOTO_ID_5114970841008279730
style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFkSIx2BvhY8hZH68cBWWmsX4PxXCt2yp-XX-G1TXza6nUQ7UOVvPCfRmNtFhDgSqwU9LJWpuIuFa07AUHib9eF3vmRk7GdATnAMvX2t0wMewnbKBg6t2rf5oK6_Bi2hySbmPs/s1600-h/Mesquite.jpg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
The latest version of the David and Wayne Maddison\'s
[Cartographer](http://mesquiteproject.org/packages/cartographer/) module
for their program [Mesquite](http://mesquiteproject.org/) can export KML
files for Google Earth. They graciously acknowledge [my crude
efforts](http://iphylo.blogspot.com/2007/06/earth-not-flat-official.html)
in this direction, and Bill Piel\'s work \-- he really started this
whole thing rolling.  
  
So, those of you inspired to try your hand at Google Earth trees, and
who were frustrated by the lack of tools should grab a copy of Mesquite
and take it for a spin.  
  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhDyGk5aXhA5bWTHX8OBlvLpg1TcZTxIB4tbe8aoqs5VJEP9tigsZt86GEoxmWl0T4aYTZ6EnLpPq8obc99m3AzU4d3jVU2HRpFcPjUPjuKvBfYSUp9OPlKFDT1n7OSPsyYGYV/s320/greatCircle-1.jpg){#BLOGGER_PHOTO_ID_5114970991332135106
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhDyGk5aXhA5bWTHX8OBlvLpg1TcZTxIB4tbe8aoqs5VJEP9tigsZt86GEoxmWl0T4aYTZ6EnLpPq8obc99m3AzU4d3jVU2HRpFcPjUPjuKvBfYSUp9OPlKFDT1n7OSPsyYGYV/s1600-h/greatCircle-1.jpg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}


The latest version of the David and Wayne Maddison's Cartographer module for their program Mesquite can export KML files for Google Earth. They graciously acknowledge my crude efforts in this direction, and Bill Piel's work -- he really started this whole thing rolling.  So, those of you inspired to try your hand at Google Earth trees, and who were frustrated by the lack of tools should grab a copy of Mesquite and take it for a spin.

Messaggi di Rogue Scholar

Progress on a phylogeny wiki

Mesquite does Google Earth files