mILD: matrix-based ILD analyses
Paul J. Planet, MD, PhD
Indra Neil Sarkar, PhD
Division of Invertebrate Zoology
American Museum of Natural History
Central Park West at 79th Street
New York, NY 10024 USA

Pairwise comparisons of disagreement in phylogenetic datasets offer a powerful tool for isolating historical incongruence for closer analysis. Statistically significant phylogenetic 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 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.

mILD requires the command line version of PAUP* to be installed on your OS X or UNIX machine. mILD is not designed to work with either the PC or Mac OS 9 versions of PAUP*. For purchase and support information with respect to PAUP*, visit: http://paup.csit.fsu.edu.

Click here for Download and Installation Information.
PLEASE READ THIS FILE BEFORE DOWNLOADING AND INSTALLING mILD!

Click here to download the OS X Installer
This file is a compressed tar-balled archive (.tgz).

Click here to download the UNIX Source Code Distribution
This file is a compressed tar-balled archive (.tgz).

Click here to download the Example dataset
This file is described in the download and installation information.