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Genetics and Molecular Research 6 (3): 522-533 (2007) FUNPEC-RP www.funpecrp.com.br Evolutionary tree reconstruction using structural
 

Summary: Genetics and Molecular Research 6 (3): 522-533 (2007) FUNPEC-RP www.funpecrp.com.br
Evolutionary tree reconstruction using structural
expectation maximization and homotopy
J. Li and M. Guo
School of Computer Science and Technology, Harbin Institute of Technology,
Harbin, China
Corresponding author: J. Li
E-mail: lijianfu@hit.edu.cn or jianfu_lili@163.com
ABSTRACT. The evolutionary tree reconstruction algorithm called SEM-
PHY using structural expectation maximization (SEM) is an efficient ap-
proach but has local optimality problem. To improve SEMPHY, a new al-
gorithm named HSEMPHY based on the homotopy continuation principle
is proposed in the present study for reconstructing evolutionary trees. The
HSEMPHY algorithm computes the condition probability of hidden vari-
ables in the structural through maximum entropy principle. It can reduce the
influence of the initial value of the final resolution by simulating the process
of the homotopy principle and by introducing the homotopy parameter .
HSEMPHY is tested on real datasets and simulated dataset to compare with
SEMPHY and the two most popular reconstruction approaches PHYML
and RAXML. Experimental results show that HSEMPHYis at least as good

  

Source: Anisimova, Maria - Institute of Scientific Computing, Eidgenössische Technische Hochschule Zürich (ETHZ)

 

Collections: Biology and Medicine