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ZOOLOGICAL RESEARCH    2013, Vol. 34 Issue (6) : 640-650     DOI: 10.11813/j.issn.0254-5853.2013.6.0640
Review |
A bird’s eye view of the algorithms and software packages for reconstructing phylogenetic trees
Li-Na ZHANG1, Chang-He RONG2, Yuan HE1, Qiong GUAN4, Bin HE4, Xing-Wen ZHU1, Jia-Ni LIU4, Hong-Ju CHEN3,4
1. Mathematics and Computer Science College, Dali University, Dali Yunnan 671003, China;
2. Yunnan Forestry Technological College, Kunming Yunnan 650224, China;
3. College of Mathematics, Honghe University, Mengzi Yunnan 661100, China;
4. Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
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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.

Keywords Phylogenetic tree      Distance matrix      Maximum parsimony      Maximum likelihood      Bayesian framework      Phylogenetic analysis software     
PACS:  Q332  
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Chang-He RONG
Yuan HE
Qiong GUAN
Bin HE
Xing-Wen ZHU
Jia-Ni LIU
Hong-Ju CHEN
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Li-Na ZHANG,Chang-He RONG,Yuan HE, et al. A bird’s eye view of the algorithms and software packages for reconstructing phylogenetic trees[J]. ZOOLOGICAL RESEARCH, 2013, 34(6): 640-650.
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