Phylogenetic methods have recently been rediscovered in several interesting areas among which immunodynamics, epidemiology and many branches of evolutionary dynamics. In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence, a divergence arises between the true evolutionary distances and the distances between pairs of taxa as inferred from the available data, making the phylogenetic reconstruction a challenging problem. Mathematically this divergence translates in the non-additivity of the actual distances between taxa and the quest for new algorithms able to efficiently cope with these effects is wide open. In distance-based reconstruction methods, two properties of additive distances were extensively exploited as antagonist criteria to drive phylogeny reconstruction: on the one hand a local property of quartets, i.e. sets of four taxa in a tree, the four-point condition; on the other hand, a recently proposed formula that allows to write the tree length as a function of the distances between taxa, the Pauplin's formula. A deeper comprehension of the effects of the non-additivity on the inspiring principles of the existing reconstruction algorithms is thus of paramount importance. In this paper we present a comparative analysis of the performances of the most important distance-based phylogenetic algorithms. We focus in particular on the dependence of their performances on two main sources of non-additivity: back-mutation processes and horizontal transfer processes. The comparison is carried out in the framework of a set of generative algorithms for phylogenies that incorporate non-additivity in a tunable way. © 2010 World Scientific Publishing Company.

Distance-based phylogenetic algorithms: New insights and applications / Caglioti, Emanuele; Loreto, Vittorio; S., Pompei; Tria, Francesca. - In: MATHEMATICAL MODELS AND METHODS IN APPLIED SCIENCES. - ISSN 0218-2025. - 20:SUPPL. 1(2010), pp. 1511-1532. [10.1142/s0218202510004672]

Distance-based phylogenetic algorithms: New insights and applications

CAGLIOTI, Emanuele;LORETO, Vittorio;TRIA, FRANCESCA
2010

Abstract

Phylogenetic methods have recently been rediscovered in several interesting areas among which immunodynamics, epidemiology and many branches of evolutionary dynamics. In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence, a divergence arises between the true evolutionary distances and the distances between pairs of taxa as inferred from the available data, making the phylogenetic reconstruction a challenging problem. Mathematically this divergence translates in the non-additivity of the actual distances between taxa and the quest for new algorithms able to efficiently cope with these effects is wide open. In distance-based reconstruction methods, two properties of additive distances were extensively exploited as antagonist criteria to drive phylogeny reconstruction: on the one hand a local property of quartets, i.e. sets of four taxa in a tree, the four-point condition; on the other hand, a recently proposed formula that allows to write the tree length as a function of the distances between taxa, the Pauplin's formula. A deeper comprehension of the effects of the non-additivity on the inspiring principles of the existing reconstruction algorithms is thus of paramount importance. In this paper we present a comparative analysis of the performances of the most important distance-based phylogenetic algorithms. We focus in particular on the dependence of their performances on two main sources of non-additivity: back-mutation processes and horizontal transfer processes. The comparison is carried out in the framework of a set of generative algorithms for phylogenies that incorporate non-additivity in a tunable way. © 2010 World Scientific Publishing Company.
2010
distance-based methods; noise and horizontal transfer; phylogeny; trees
01 Pubblicazione su rivista::01a Articolo in rivista
Distance-based phylogenetic algorithms: New insights and applications / Caglioti, Emanuele; Loreto, Vittorio; S., Pompei; Tria, Francesca. - In: MATHEMATICAL MODELS AND METHODS IN APPLIED SCIENCES. - ISSN 0218-2025. - 20:SUPPL. 1(2010), pp. 1511-1532. [10.1142/s0218202510004672]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/355279
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