Abstract
In this article we describe a new method allowing one to predict and visualize possible horizontal gene transfer events. It relies either on a metric or topological optimization to estimate the probability of a horizontal gene transfer between any pair of edges in a species phylogeny. Species classification will be examined in the framework of the complete and partial gene transfer models.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
CHARLESTON, M. A. (1998): Jungle: a new solution to the host/parasite phylogeny reconciliation problem. Math. Bioscience, 149, 191–223.
DOOLITTLE, W. F. (1999): Phylogenetic classification and the universal tree. Science, 284, 2124–2129.
GUINDON, S. and GASCUEL, O. (2003): A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol., 52, 696–704.
LAKE, J. A. and RIVERA, M. C. (2004): Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction. Mol. Biol. Evol., 21, 681–690.
LEGENDRE, P. and V. MAKARENKOV. (2002): Reconstruction of biogeographic and evolutionary networks using reticulograms. Syst. Biol., 51, 199–216.
MAKARENKOV, V. and LECLERC, B. (1999): An algorithm for the fitting of a tree metric according to a weighted LS criterion. J. of Classif., 16, 3–26.
MAKARENKOV, V. (2001): reconstructing and visualizing phylogenetic trees and reticulation networks. Bioinformatics, 17, 664–668.
MAKARENKOV, V., BOC, A. and DIALLO, A. B. (2004): Representing lateral gene transfer in species classification. Unique scenario. In: D. Banks, L. House, F. R. McMorris, P. Arabie, and W. Gaul (eds.): Classification, Clustering and Data Mining Applications. Springer Verlag, proc. IFCS 2004, Chicago 439–446
MIRKIN, B. G., MUCHNIK, I. and SMITH, T.F. (1995): A Biologically Consistent Model for Comparing Molecular Phylogenies. J. of Comp. Biol., 2, 493–507.
MORET, B., NAKHLEH, L., WARNOW, T., LINDER, C., THOLSE, A., PADOLINA, A., SUN, J. and TIMME, R. (2004): Phylogenetic Networks: Modeling, Reconstructibility, Accuracy. Trans. Comp. Biol. Bioinf., 1, 13–23.
PAGE, R. D. M. (1994): Maps between trees and cladistic analysis of historical associations among genes, organism and areas. Syst. Biol., 43, 58–77.
PAGE, R. D. M. and CHARLESTON, M. A. (1998): Trees within trees: phylogeny and historical associations. Trends Ecol. Evol., 13, 356–359.
ROBINSON, D. R. and FOULDS, L. R. (1981): Comparison of phylogenetic trees. Math. Biosciences, 53, 131–147.
TSIRIGOS, A. and RIGOUTSOS, I. (2005): A Sensitive, Support-Vector-Machine Method for the Detection of Horizontal Gene Transfers in Viral, Archaeal and Bacterial Genomes. Nucl. Acids Res., 33, 3699–3707.
WOESE, C., OLSEN, G., IBBA, M. and SÖLL, D. (2000): Aminoacyl-tRNA synthetases, genetic code, evolut. process. Micr. Mol. Biol. Rev., 64, 202–236.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin · Heidelberg
About this paper
Cite this paper
Makarenkov, V., Boc, A., Delwiche, C.F., Diallo, A.B., Philippe, H. (2006). New Efficient Algorithm for Modeling Partial and Complete Gene Transfer Scenarios. In: Batagelj, V., Bock, HH., Ferligoj, A., Žiberna, A. (eds) Data Science and Classification. Studies in Classification, Data Analysis, and Knowledge Organization. Springer, Berlin, Heidelberg . https://doi.org/10.1007/3-540-34416-0_37
Download citation
DOI: https://doi.org/10.1007/3-540-34416-0_37
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-34415-5
Online ISBN: 978-3-540-34416-2
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)