原创力文档taxon ordering in phylogenetic trees by means of evolutionary algorithms分类单元排序在系统发育树的进化算法.pdfVIP
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taxon ordering in phylogenetic trees by means of evolutionary algorithms分类单元排序在系统发育树的进化算法
Cerutti et al. BioData Mining 2011, 4:20
/content/4/1/20 BioData Mining
RESEARCH Open Access
Taxon ordering in phylogenetic trees by means
of evolutionary algorithms
Francesco Cerutti1,2, Luigi Bertolotti1,2, Tony L Goldberg3 and Mario Giacobini1,2*
* Correspondence: mario. Abstract
giacobini@unito.it
1Department of Animal Production, Background: In in a typical “left-to-right” phylogenetic tree, the vertical order of taxa
Epidemiology and Ecology, Faculty
of Veterinary Medicine, University is meaningless, as only the branch path between them reflects their degree of
of Torino, Via Leonardo da Vinci similarity. To make unresolved trees more informative, here we propose an
44, 10095, Grugliasco (TO), Italy innovative Evolutionary Algorithm (EA) method to search the best graphical
Full list of author information is
available at the end of the article representation of unresolved trees, in order to give a biological meaning to the
vertical order of taxa.
Methods: Starting from a West Nile virus phylogenetic tree, in a (1 + 1)-EA we
evolved it by randomly rotating the internal nodes and selecting the tree with better
fitness every generation. The fitness is a sum of genetic distances between the
considered taxon and the r (radius) next taxa. After having set the radius to the best
performance, we evolved the trees with (l + μ)-EAs to study the influence of
population on the algorithm.
Results: The (1 + 1)-EA consistently out
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