Center for Integrative Bioinformatics Vienna Max F. Perutz Laboratories Dr. Bohr Gasse 9 A-1030 Vienna, Austria

Welcome to PDA - Phylogenetic Diversity Analyzer Introduction: Phylogenetic Diversity (PD), coined by Faith (1992), is a quantitative measure to assess the biodiversity of species based on a phylogeny. Given n taxa (or species) connected in a phylogenetic tree, the PD of any subset of taxa is defined as the sum of the branch-lengths of the minimal subtree connecting these taxa. We have recently proposed an extension of PD for split networks (or split systems). Given a split system of n taxa, the PD of any subset of taxa is equal to the sum of the weights of all the splits separating at least two taxa in the subset. This definition coincides with the tree-based PD when the underlying split system turns out to be a tree. Phylogenetic Diversity Analyzer (PDA) is a software tool to analyze various aspects of PD and PD-related measures based on both phylogenetic trees and networks. The major features include: Determining the taxon set of a given size k with optimal PD (maximal or minimal) for both trees and networks. Algorithms implemented include gPDA and pPDA for trees, PD-NET for circular split networks. Determining the taxon set with optimal PD (maximal or minimal) under budget constraints for both trees and networks. Algorithms implemented include PD-NET-BUDGET. Computing the PD scores of predefined areas (an area is simply a set of taxa, such as the taxa living in the area). PDA also includes the computation of exclusive PD, PD-Endemism, PD-Complementarity. Distinguishing between unrooted-PD and rooted-PD. NEWS: A new user-friendly web-interface is available at http://www.cibiv.at/software/pda/web-pda/ Download: We are please to announce that PDA version 0.5.1 (2008-04-22) is now ready for download free of charge. At the moment only the source code is available. We will make the executable binaries for Linux, Windows, and MacOS soon. Note that you can also use the web-interface at the above link. Choose the following links for downloading suitable packages: pda-0.5.1.tar.gz (Source code only, gzipped TAR format) Click here for older versions Documentation: User Manual version 0.5.1 (updated Apr 2008): in HTML format or in PDF format Reference: The methods are described in detail in the following articles: B.Q. Minh, S. Klaere, and A. von Haeseler (2006) Phylogenetic Diversity within Seconds. Syst. Biol., 55, 769-773. (DOI: 10.1080/10635150600981604) B.Q. Minh, F. Pardi, S. Klaere, and A. von Haeseler (2008) Budgeted Phylogenetic Diversity on Circular Split Systems. IEEE/ACM Trans. Comput. Biol. Bioinform., 5, in press. (DOI: 10.1109/TCBB.2008.54) A manuscript describing the split diversity method is submitted. Note: Please, let us know if you download this program by sending an email to {minh.bui, steffen.klaere, tung.nguyen, arndt.von.haeseler}(at)univie.ac.at