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Updated: May 4, 2026

A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
[A bird's eye view of the algorithms and software packages for reconstructing phylogenetic trees]
Li-Na Zhang1, Chang-He Rong, Yuan He
1Computational 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. chenhongju_teacher@hotmail.com.
Abstract:
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.
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