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Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution.
KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
Stockholm Bioinformatics Center, Dept. of Biochemistry, Stockholm University.
KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
2004 (English)In: Proceedings of the Annual International Conference on Computational Molecular Biology, RECOM, 2004, 326-335 p.Conference paper (Refereed)
Abstract [en]

Gene tree and species tree reconstruction, orthology analysis and reconciliation, are problems important in multigenome-based comparative genomics and biology in general. In the present paper, we advance the frontier of these areas in several respects and provide important computational tools. First, exact algorithms are given for several probabilistic reconciliation problems with respect to the probabilistic gene evolutionmodel, previously developed by the authors. Until now, those problems were solved by MCMC estimation algorithms. Second, we extend the gene evolution model to the genesequence evolution model, by including sequence evolution. Third, we develop MCMC algorithms for the gene sequence evolution model that, given gene sequence data allows: (1) orthology analysis, reconciliation analysis, and gene tree reconstruction, w.r.t. a species tree, that balances a likely/unlikely reconciliation and a likely/unlikely genetree and (2) species tree reconstruction that balance a likely /unlikely reconciliation and a likely/unlikely gene trees. These MCMC algorithms take advantage of the exact algorithms for the gene evolution model. We have successfully tested our dynamical programming algorithms on real data for a biogeography problem. The MCMC algorithms perform very well both on synthetic and biological data.

Place, publisher, year, edition, pages
2004. 326-335 p.
Keyword [en]
Algorithms, baysian analysis, gene tree, orthology, reconciliation
National Category
Computer and Information Science
URN: urn:nbn:se:kth:diva-61190ScopusID: 2-s2.0-2442562450OAI: diva2:478711
RECOMB '04: Proceedings of the eighth annual international conference on Resaerch in computational molecular biology, San Diego, CA.; 27 March 2004 through 31 March 2004
QC 20120117Available from: 2012-01-16 Created: 2012-01-16 Last updated: 2012-01-17Bibliographically approved

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