Padre

Package for Analyzing and Displaying Reticulate Evolution (Padre) is a Java program for computing phylogenetic networks from rooted multi-labelled phylogenetic trees.

PADRE: Package for Analyzing and Displaying Reticulate Evolution

Description

PADRE is a Java software package allowing the computation and graphical representation of reticulate networks from (a collection of) multi-labelled trees. If a collection of trees are loaded, the software first performs a consensus from which a collection of consensus trees are constructed. Finally, one of the consensus trees can be used to construct a reticulate network. In case a single tree is loaded, the consensus stage is skipped and the reticulate network is constructed directly from that tree. A range of user specified options are provided for both the consensus and network construction methods.

Input to the program takes the form of text files containing (a collection of) multi-labelled trees in the widely used NEWICK format (as described by The Newick Tree Format) see our test files for examples. The program is available as a complied JAR file which is platform independent and suitable for running on Windows, Linux and MacOS. Images may be exported to EPS, PNG and JPEG format suitable for inclusion in publications. All tree and network representations are initially scaled to fit the screen, vertices (and the edges connected to them) may be dragged and dropped anywhere on screen.

If you use PADRE we would appreciate if you could cite the following paper:

K. T. Huber, B. Oxelman, M. Lott and V. Moulton, Reconstructing the evolutionary history of polyploids from multi-labelled trees, Mol Biol Evol 2006 23: 1784-1791

Availability

PADRE is written in Java, and the most recent version, version 2.0, is compiled using J2SE 5.0 - the application is standalone but if you are having problems running it please ensure you have Java Virtual Machine (VM) version 5.0 or above installed.

Once you have a suitable Java VM installed, download the ZIP file (ZIP, 2Mb) containing PADRE and its dependencies. The PADRE JAR file within this ZIP file includes a manifest enabling it to be run from the command line using java -Xmx1400m -jar padre.jar. Using this command line argument helps avoid out of memory errors (indicated by java.lang.OutOfMemoryError displayed in the terminal window).

We have also developed a command line version (ZIP, 2.14Mb) suitable for use as part of a pipeline or for processing difficult datasets on a cluster.

Manual

Usage of the program is described in the PADRE manual (PDF,182Kb) available to download.

Test files

We have also included a number of test files in NEWICK format with the PADRE program:

Consensus method test files used in publication [3] listed below:

Dataset 1 - Six trees constructed for a Silene dataset including two trees which are 'partial' and may be considered to be phylogenetic trees in the usual sense.

Dataset 2 - Four trees, again based on a Silene dataset, though they are larger than those in the previous example and are very unresolved.

Network construction method test files used in publication [1] listed below:

Figure 3 -The multi-labelled tree depicted in Figure 3 of publication [1].

Figure 5 -The multi-labelled tree depicted in Figure 5 of publication [1].

Support

For technical questions or feature requests, e-mail Martin Lott.

References

K. T. Huber, B. Oxelman, M. Lott and V. Moulton, Reconstructing the evolutionary history of polyploids from multi-labelled trees, Molecular Biology and Evolution 2006 23(9): 1784-1791.

K. T. Huber, M. Lott, V. Moulton and A. Spillner, The Complexity of Deriving Multi-Labeled Trees from Bipartitions, Journal of Computational Biology 2008 15(6): 639-651.

M. Lott, A. Spillner, K. T. Huber, V. Moulton, A. Petri and B. Oxelman, Inferring polyploid phylogenies from multiply-labeled gene trees, Submitted.

M. Lott, A. Spillner, K. T. Huber and V. Moulton, PADRE: A Package for Analyzing and Displaying Reticulate Evolution, Submitted.

Supporting material

Valiente, G, Algorithms on Trees and Graphs, Springer-Verlag, 2002.

Disclaimer

This software is supplied as-is, with no warranty of any kind expressed or implied. We have made every effort to avoid errors in design and execution of this software, but we will not be liable for its use or misuse. The user is solely responsible for the validity and consequences of any results generated.

Research Team

Martin Lott, Prof. Vincent Moulton, Dr. Katharina Huber

PADRE is released under the GNU General Public License, the source code is freely available here to modify providing the copyright notice remains intact and due credit is given to the authors in publications.