Efficient Enumeration of the Directed Binary Perfect Phylogenies from Incomplete Data
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- 作者：Masashi Kiyomi (1)
Yoshio Okamoto (2)
Toshiki Saitoh (3) - 刊名：Lecture Notes in Computer Science
- 出版年：2012
- 出版时间：2012
- 年：2012
- 卷：7276
- 期：1
- 页码：248-259
- 全文大小：249.4 KB
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- 刊物类别：Computer Science
- 刊物主题：Artificial Intelligence and Robotics
Computer Communication Networks
Software Engineering
Data Encryption
Database Management
Computation by Abstract Devices
Algorithm Analysis and Problem Complexity - 出版者：Springer Berlin / Heidelberg
- ISSN：1611-3349
文摘
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.