Skip Navigation



Bioinformatics Advance Access published online on November 2, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti744
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/24/4423    most recent
bti744v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Planet, P. J.
Right arrow Articles by Sarkar, I. N.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Planet, P. J.
Right arrow Articles by Sarkar, I. N.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received August 2, 2005
Revised October 7, 2005
Accepted October 24, 2005

Applications note

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

Paul J. Planet 1 and Indra Neil Sarkar 2*

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

* To whom correspondence should be addressed.
Indra Neil Sarkar, E-mail: sarkar{at}amnh.org


  Abstract

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*.

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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


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]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.