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Bioinformatics Advance Access originally published online on November 2, 2005
Bioinformatics 2005 21(24):4423-4424; doi:10.1093/bioinformatics/bti744
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

mILD: a tool for constructing and analyzing matrices of pairwise phylogenetic character incongruence tests

Paul J. Planet 1 and Indra Neil Sarkar 1,2,*

1Division of Invertebrate Zoology, American Museum of Natural History New York, NY, USA
2Division of Library Services, American Museum of Natural History New York, NY, USA

*To whom correspondence should be addressed.

Summary: Pairwise comparisons of disagreement in phylogenetic datasets offer a powerful tool for isolating historical incongruence for closer analysis. Statistically significant phylogenetic character incongruence may reflect important differences in evolutionary history, such as horizontal gene transfer. Such testing can also be used to specify possible combinations of datasets for further phylogenetic analysis. The process of comparing multiple datasets can be very time consuming, and it is sometimes unclear how to combine data partitions given the observed patterns of incongruence. Here we present an application that automates the process of making pairwise comparisons between large numbers of phylogenetic datasets using the Incongruence Length Difference (ILD) test. The application also implements strategies for data combination based on the patterns of incongruence observed in pairwise comparisons.

Availability: The application is freely available as a Perl script that interacts with the command-line version of PAUP*.

Contact: sarkar{at}amnh.org

Supplementary information: http://www.GenomeCurator.org/mILD/

Received on August 2, 2005; revised on October 7, 2005; accepted on October 24, 2005

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This article has been cited by other articles:


Home page
 Syst BiolHome page
D. L. J. Quicke, O. R. Jones, and D. R. Epstein
Correcting the Problem of False Incongruence Due to Noise Imbalance in the Incongruence Length Difference (ILD) Test
Syst Biol, June 1, 2007; 56(3): 496 - 503.
[Abstract] [Full Text] [PDF]


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