Phylogenetic systematics is the study of evolutionary relations between species based on their shared traits. Represented diagrammatically, these relations can form a tree whose leaves represent the species, internal vertices represent their ancestors, and edges represent the genetic relationships between them. Such a tree is called a "phylogenetic tree" (or a "phylogeny").We consider reconstruction of phylogenies as the first step of reconstructing the evolutionary history of a set of taxa (taxonomic units). The idea is then to reconstruct (temporal) phylogenetic networks, which also explain the contacts (or borrowings) between taxonomic units, from the reconstructed phylogenies. We have studied both steps using computational methods of Answer Set Programming (ASP): the first step is studied in [1,2,3,5], and the second step is studied in [4]. We have also studied the comparison of phylogenies using ASP [6,9,12] and reconstruction of weighted phylogenies [8,10,11]. We call our ASP-based approach to (weighted) phylogenetic tree reconstruction/comparison as Phylo-ASP [8].

COMPUTATIONAL TOOLS




As a part of Phylo-ASP, we provide the following computational tools:

PhyloReconstruct-ASP: An ASP-based system for reconstructing phylogenies.
PhyloAnalyze-ASP: An ASP-based system for analyzing phylogenies.
PhyloReconstructN-ASP: An ASP-based system for reconstructing similar/diverse phylogenies.
PhyloCompare-ASP: An ASP-based system for comparing phylogenies.

ACKNOWLEDGEMENTS




This work has been supported by TUBITAK Grant 107E229.

PUBLICATIONS





[1] E. Erdem, V. Lifschitz, L. Nakhleh, D. Ringe. Reconstructing the evolutionary history of Indo-European languages using answer set programming. In Proc. of PADL, 2003.

[2] D. Brooks, E. Erdem, J. Minett, D. Ringe. Character-based cladistics and answer set programming. In Proc. of PADL, 2005.

[3] E. Erdem, F. Wang. Reconstructing the evolutionary history of Chinese dialects. Accepted for presentation at the 39th International Conference on Sino-Tibetan Languages and Linguistics, ICSTLL, 2006.

[4] E. Erdem, V. Lifschitz, D. Ringe. Temporal phylogenetic networks and logic programming. Theory and Practice of Logic Programming 6(5), 539-558, 2006.

[5] D. Brooks, E. Erdem, S. Erdogan, J. Minett, and D. Ringe. Inferring phylogenetic trees using answer set programming. In Journal of Automated Reasoning, Vol. 39(4), pp. 471-511, 2007.

[6] T. Eiter, E. Erdem, H. Erdogan, and M.Fink. Finding Similar or Diverse Solutions in Answer Set Programming. In Proc. of ICLP, 2009.

[7] D. Cakmak, E. Erdem, and H. Erdogan. Computing Weighted Solutions in Answer Set Programming. In Proc. of LPNMR, 2009.

[8] E. Erdem. PHYLO-ASP: Phylogenetic Systematics with Answer Set Programming. In Proc. of LPNMR, 2009.

[9] H. Erdogan. Quantifying solutions in answer set programming. In Proc. of CSW, 2010.

[10] D. Cakmak and E. Erdem and H. Erdogan. Computing Weighted Solutions in ASP: Representation-Based Method vs. Search-Based Method. In Proc. of RCRA, 2010.

[11] D. Cakmak and E. Erdem and H. Erdogan. Computing Weighted Solutions in ASP: Representation-Based Method vs. Search-Based Method. In Annals of Mathematics and Artificial Intelligence, 2011.

[12] T. Eiter, E. Erdem, H. Erdogan, and M.Fink. Finding Similar or Diverse Solutions in Answer Set Programming. In Theory and Practice of Logic Programming, 2011.