utcs Phylogenetics
Research · Publications · Software · People ·
Datasets

Supertree Estimation Datasets

Overview

This page contains datasets that may be useful for testing supertree methods, which combine a set of phylogenies into a single estimated phylogeny on the intersection of the taxa appearing in the input set [16]. In addition to sets of supertree inputs, the simulated datasets contain model (true) trees that can be used to assess supertrees' accuracy. Assessing accuracy on empirical datasets, however, is somewhat problematic [2]. If you would like to contribute benchmarks to this resource, please email tandy@cs.utexas.edu.

Simulated Data

SMIDGen: SMIDGen is a methodology for generating simulated datasets suitable as inputs to supertree methods. The data generation process mirrors data collection processes used by systematists when gathering empirical data, including creation of densely-sampled clade-based trees as well as sparsely-sampled scaffold trees.
Described in [1]
Studied in [2]

Empirical Data

Comprehensive papilionoid legumes: CPL.tar.gz
2228 taxa, 39 source trees estimated using RAxML [15]
Described in [4]
Studied in [4]

Marsupials: marsupials.tar.gz
267 taxa, 158 source trees
Described in [5]
Studied in [5, 9, 10, 11, 12, 13, 14]

Placental mammals: placental mammals.tar.gz
116 taxa, 726 source trees
Described in [6]
Studied in [6, 9]

Seabirds: seabirds.tar.gz
121 taxa, 7 source trees
Described in [7]
Studied in [7, 9]

Temperate herbaceous papilionoid legumes: THPL.tar.gz
558 taxa, 19 source trees
Described in [8]
Studied in [8, 9, 10, 12]

References

Disclaimer

Links to external web sites are for datasets and software available through other laboratories and organizations. The respective labs and organizations are responsible for these datasets and software; please contact them if you have any problems or questions regarding their material. If you experience any problems with our datasets or software, please feel free to contact us at tandy@cs.utexas.edu.
Copyright © 2009-2010 Computational Phylogenetics Lab | ACES 3.304 | University of Texas | Austin, TX 78712
Site help/questions/feedback/requests: e-mail Tandy Warnow