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The aim of this paper is to enable those who have never reconstructed a phylogeny to do so from scratch. The paper does not attempt to be a comprehensive theoretical guide, but describes one rigorous way of obtaining phylogenetic trees. Those who follow the methods outlined should be able to understand the basic ideas behind the steps taken, the meaning of the phylogenetic trees obtained and the scope of questions that can be answered with phylogenetic methods. The protocols have been successfully tested by volunteers with no phylogenetic experience.

Original publication




Journal article


Plant J

Publication Date





561 - 572


Amino Acid Sequence, Base Sequence, DNA, Plant, Likelihood Functions, Molecular Sequence Data, Phylogeny, Plants, Sequence Homology, Amino Acid