Efficient enumeration of the directed binary perfect phylogenies from incomplete data

Authors:
Masashi Kiyomi;Yoshio Okamoto;Toshiki Saitoh
Affiliations:
School of Information Science, Japan Advanced Institute of Science and Technology, Nomi, Japan;Center for Graduate Education Initiative, Japan Advanced Institute of Science and Technology, Nomi, Japan;ERATO Minato Discrete Structure Manipulation System Project, Japan Technology and Science Agency, Sapporo, Japan
Venue:
SEA'12 Proceedings of the 11th international conference on Experimental Algorithms
Year:
2012

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Abstract

We study a character-based phylogeny reconstruction problem when an incomplete set of data is given. More specifically, we consider the situation under the directed perfect phylogeny assumption with binary characters in which for some species the states of some characters are missing. Our main object is to give an efficient algorithm to enumerate (or list) all perfect phylogenies that can be obtained when the missing entries are completed. While a simple branch-and-bound algorithm (B&B) shows a theoretically good performance, we propose another approach based on a zero-suppressed binary decision diagram (ZDD). Experimental results on randomly generated data exhibit that the ZDD approach outperforms B&B. We also prove that counting the number of phylogenetic trees consistent with a given data is #P-complete, thus providing an evidence that an efficient random sampling seems hard.