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Gene. 2013 Sep 15;527(1):344-51. doi: 10.1016/j.gene.2013.06.036. Epub 2013 Jun 28.

BIMLR: a method for constructing rooted phylogenetic networks from rooted phylogenetic trees.

Author information

1
School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, PR China. wangjuanangle@hit.edu.cn

Abstract

Rooted phylogenetic trees constructed from different datasets (e.g. from different genes) are often conflicting with one another, i.e. they cannot be integrated into a single phylogenetic tree. Phylogenetic networks have become an important tool in molecular evolution, and rooted phylogenetic networks are able to represent conflicting rooted phylogenetic trees. Hence, the development of appropriate methods to compute rooted phylogenetic networks from rooted phylogenetic trees has attracted considerable research interest of late. The CASS algorithm proposed by van Iersel et al. is able to construct much simpler networks than other available methods, but it is extremely slow, and the networks it constructs are dependent on the order of the input data. Here, we introduce an improved CASS algorithm, BIMLR. We show that BIMLR is faster than CASS and less dependent on the input data order. Moreover, BIMLR is able to construct much simpler networks than almost all other methods. BIMLR is available at http://nclab.hit.edu.cn/wangjuan/BIMLR/.

KEYWORDS:

Evolution; Molecular evolution; Phylogenetic; e.g.; exempli gratia; i.e.; id est; w.r.t; with regard to

PMID:
23816409
DOI:
10.1016/j.gene.2013.06.036
[Indexed for MEDLINE]
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