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Zoological Research
Kunming Institute of Zoology, Chinese Academy of Sciences
ISSN: 2095-8137
Vol. 34, No. 6, 2013, pp. 640-650
Bioline Code: zr13101
Full paper language: English
Document type: Review Article
Document available free of charge

Zoological Research, Vol. 34, No. 6, 2013, pp. 640-650

 en A bird's eye view of the algorithms and software packages for reconstructing phylogenetic trees
ZHANG, Li-Na; RONG, Chang-He; HE, Yuan; GUAN, Qiong; HE, Bin; ZHU, Xing-Wen; LIU, Jia-Ni & CHEN, Hong-Ju


The prototype phylogenetic tree, i.e., evolutionary "tree" or "tree of life", was first conceived by Charles Darwin in his seminal book "The Origin of Species", and its reconstructions have been approached by generations of biologists ever since. In this article, we briefly reviewed the major algorithms and software packages for reconstructing phylogenetic trees. Specifically we discuss four categories of phylogeny algorithms including distance-matrix, maximum parsimony, maximum likelihood, and Bayesian framework, as well as software packages (PHYLIP, MEGA, MrBayes) based on them.

Phylogenetic tree; Distance matrix; Maximum parsimony; Maximum likelihood; Bayesian framework; Phylogenetic analysis software

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