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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 0.5.2 (2011-08-01) is now ready for download. This version fixes some
compatibility issues with the newer GCC compiler.
Choose the following links for downloading suitable packages:
Click here for older versions
Documentation:
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 (2009)
Budgeted Phylogenetic Diversity on Circular Split Systems.
IEEE/ACM Trans. Comput. Biol. Bioinform., 6, 22-29.
(DOI: 10.1109/TCBB.2008.54,
PMID: 19179696)
- B. Q. Minh, S. Klaere, and A. von Haeseler (2009)
Taxon Selection under Split Diversity.
Syst. Biol., 57, 586-594.
(DOI: 10.1093/sysbio/syp058)
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
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