Coronavirus phylogeny based on Base-Base Correlation
International Journal of Bioinformatics Research and Applications
Whole-genome prokaryotic clustering based on gene lengths
Discrete Applied Mathematics
A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
Robust classifying of prokaryotic genomes
Computational Biology and Chemistry
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Summary: Comparing gene content between species can be a useful approach for reconstructing phylogenetic trees. In this paper, we derive a maximum-likelihood estimation of evolutionary distance between species under a simple model of gene genesis and gene loss. Using simulated data on a biological tree with 107 taxa (and on a number of randomly generated trees), we compare the accuracy of tree reconstruction using this ML distance measure to an earlier ad hoc distance. We then compare these distance-based approaches to a character-based tree reconstruction method (Dollo parsimony) which seems well suited to the analysis of gene content data. To simplify simulations, we give a formal proof of the well-known 'fact' that the Dollo parsimony score is independent of the choice of root. Our results show a consistent trend, with the character-based method and ML distance measure outperforming the earlier ad hoc distance method. Availability: http://www.ab.informatik.uni-tuebingen.de/software/genecontent/welcome_en.html