http://phylotastic.or g /. A project of the NESCent HIP (hackathons, interoperability, phyogenies) working group. Making the Tree of Life Accessible for Research.
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A project of the NESCent HIP (hackathons, interoperability, phyogenies) working group.
Making the Tree of Life Accessible for Research
This is a 20-minute overview with links to screencasts and demos, providing an introduction to the project and to the upcoming 2nd hackathon (Jan 28 to Feb 1, 2013, Tucson, AZ).
“Most attempts at re-use seem to end in disappointment” 
 Stoltzfus, et al., 2012, “Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis”, http://www.ncbi.nlm.nih.gov/sites/entrez/23088596
. . .
R.L. Walls with Linnaeus
Input list from Walls, 2011
98-species tree of Walls, 2011
APG framework with 1566 taxa
* Proper phylogenies as well as phylogeny-based taxonomic hierarchies
* Hackathons, Interoperability, Phylogenies, a NESCent working group
It’s all open source
Screencasts & live demonstrations
my $base = "http://phylotastic-wg.nescent.org/script/phylotastic.cgi";
my ( $tree, $taxa ) = @ARGV;
$taxa =~ s/[ _]/+/g;
$taxa =~ s/,/%2C/g;
system( "curl \"$base?species=$taxa&tree=$tree&format=newick\" > out.tre; open out.tre" );
36 species + 2 extras*
auto-extract species names from text
Copy & paste species named in Table 1
Riek, 2011 (Mammalian Biology 76(1):3-11)
Manually key in species list from tree image
Hours or days
Manually reconcile names with names in source tree
* named in text but not used in phylogenetic analysis
r8s, pathd8, Multidivtime
Calibrating a tree using fossil timepoints
(R, FastRWeb, Rserve)
Branches could shift without warning
There are some holes
You might crash
We haven’t put the pieces together yet
The interfaces are unstable
Send feedback to Arlin Stoltzfus ([email protected])
HIP Leadership Team