Simultaneous Bayesian gene tree reconstruction and reconciliation analysis
نویسندگان
چکیده
منابع مشابه
Simultaneous Bayesian gene tree reconstruction and reconciliation analysis.
We present GSR, a probabilistic model integrating gene duplication, sequence evolution, and a relaxed molecular clock for substitution rates, that enables genomewide analysis of gene families. The gene duplication and loss process is a major cause for incongruence between gene and species tree, and deterministic methods have been developed to explain such differences through tree reconciliation...
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MOTIVATION BUCKy is a C++ program that implements Bayesian concordance analysis. The method uses a non-parametric clustering of genes with compatible trees, and reconstructs the primary concordance tree from clades supported by the largest proportions of genes. A population tree with branch lengths in coalescent units is estimated from quartet concordance factors. AVAILABILITY BUCKy is open s...
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MOTIVATION Comparative genomics in general and orthology analysis in particular are becoming increasingly important parts of gene function prediction. Previously, orthology analysis and reconciliation has been performed only with respect to the parsimony model. This discards many plausible solutions and sometimes precludes finding the correct one. In many other areas in bioinformatics probabili...
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Gene tree/species tree reconciliation is a recent decisive progress in phylogenetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by gene-scale events such as duplication, loss, transfer, which translates mathematically into a mapping between gene tree nodes and species tree nodes or branche...
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ژورنال
عنوان ژورنال: Proceedings of the National Academy of Sciences
سال: 2009
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.0806251106