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BMC Systems Biology

, 5:S2

First Online: 23 December 2011

Abstract

BackgroundA phylogenetic tree, showing ancestral relations among organisms, is commonly represented as a rooted tree with sets of bifurcating branches dichotomies for simplicity, although polytomies multifurcating branches may reflect more accurate evolutionary relationships. To represent the true evolutionary relationships, it is important to systematically identify the polytomies from a bifurcating tree and generate a taxonomy-compatible multifurcating tree. For this purpose we propose a novel approach -PolyPhy-, which would classify a set of bifurcating branches of a phylogenetic tree into a set of branches with dichotomies and polytomies by considering genome distances among genomes and tree topological properties.

ResultsPolyPhy employs a machine learning technique, BLR Bayesian logistic regression classifier, to identify possible bifurcating subtrees as polytomies from the trees resulted from ComPhy. Other than considering genome-scale distances between all pairs of species, PolyPhy also takes into account different properties of tree topology between dichotomy and polytomy, such as long-branch retraction and short-branch contraction, and quantifies these properties into comparable rates among different sub-branches. We extract three tree topological features -LR- Leaf rate -IntraR- Intra-subset branch rate and -InterR- Inter-subset branch rate, all of which are calculated from bifurcating tree branch sets for classification. We have achieved F-measure balanced measure between precision and recall of 81% with about 0.9 area under the curve AUC of ROC.

ConclusionsPolyPhy is a fast and robust method to identify polytomies from phylogenetic trees based on genome-wide inference of evolutionary relationships among genomes. The software package and test data can be downloaded from http:-digbio.missouri.edu-ComPhy-phyloTreeBiNonBi-1.0.zip.

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Author: Guan Ning Lin - Chao Zhang - Dong Xu

Source: https://link.springer.com/



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