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Stability Analysis of Phylogenetic Trees

Phylogenetics, or reconstructing the evolutionary history of organisms, is critical for understanding evolution. A large number of heuristic algorithms for phylogenetics have been developed, some of which enable estimates of trees with tens of thousands of taxa. Such trees may not be {\em robust}, as small changes in the input data can cause major differences in the optimal topology. Tools that can assess the quality and stability of phylogenetic tree estimates and identify the most reliable parts of the tree are needed. In this project, we define measures that assess the stability of trees, subtrees and individual taxa with respect to changes in the input sequence(s). Our measures consider changes at the finest granularity in the input data (i.e., individual nucleotides). We demonstrate the effectiveness of our measures on large published datasets. Our measures are computationally feasible for phylogenetic datasets consisting of tens of thousands of taxa.

Keywords: Phylogenetics, Evolution, Stability, Robustness, Post-Optimality Analysis.
Download the phylogenetic stability software. [README]


Tamer Kahveci
Last modified: Wed Nov 28 18:03:26 EST 2012