Abstract:
DateLife.org is a new service that allows users to upload a list of two or more taxon names and return distributions of the ages of their most common ancestor, as well as the pruned chronograms that have those taxa. It thus allows real-time synthesis of information from existing studies to estimate divergence times, which is essential for many scientific analyses incorporating phylogenies. Importantly, large scale reuse, including automated queries using a RESTful interface, is encouraged. The source trees come from phylogenetic studies. If a study provides a set of trees (such as a cloud of trees from a BEAST run), credibility intervals are automatically returned to the user rather than a point estimate. DateLife is coded mostly in R using the FastRWeb and RServe packages. Its main source code is available at
https://bitbucket.org/bomeara/datelife ; its tree store comes from the PhyloOrchard package on R-forge. Currently DateLife uses 11 studies with a total of over 4000 trees (including samples from BEAST runs) for 6,973 taxa; the total number of leaves is 620,868. DateLife was created as part of the Phylotastic hackathon; as of the time of abstract submission, it is just three weeks old. Short term plans include adding taxonomic name resolution, data from fossils, many more studies, export to NExML format, and services to convert a phylogram to a chronogram using DataLife data. DateLife represents an important new step in allowing general reuse of existing phylogenetics discoveries about dates while also calculating and highlighting uncertainty in those estimates.
Authors: Brian O'Meara, Tracy Heath, Jonathan Eastman, Peter Midford, Joseph Brown, Matt Pennell, Mike Alfaro, Luke Harmon
Presenter: Brian O'Meara
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Brian O'Meara
Assistant Professor
Dept. of Ecology & Evolutionary Biology
U. of Tennessee, Knoxville
http://www.brianomeara.infoStudents wanted: Applications due Dec. 15, annually
Postdoc collaborators wanted: Check NIMBioS' website
Calendar:
http://www.brianomeara.info/calendars/omeara