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Computational Biology - Genomes, Networks, and Evolution · LibreTexts

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    Bibliography

    [1] O. Akerborg, B. Sennblad, L. Arvestad, and J. Lagergren. Bayesian gene tree reconstruction and recon- ciliation analysis. Proc Natl Acad Sci, 106(14):5714–5719, Apr 2009.

    [2] Zmasek C.M. and Eddy S.R. Analyzing proteomes by automated phylogenomics using resampled infer- ence of orthologs. BMC Bioinformatics, 3(14), 2002.

    [3] Li H, Coghlan A, Ruan J, Coin LJ, Heriche JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, DEhal P, Wang J, and Durbin R. Treefam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res, 34, 2006.

    [4] Arvestad L., Berglund A., Lagergren J., and Sennblad B. Bayesian gene/species tree reconciliation and orthology analysis using mcmc. Bioinformatics, 19 Suppl 1, 2003.

    [5] M. D. Rasmussen and M. Kellis. A bayesian approach for fast and accurate gene tree reconstruction. Mol Biol Evol, 28(1):273290, Jan 2011.

    [6] Matthew D. Rasmussen and Manolis Kellis. Accurate gene-tree reconstruction by learning gene and species-specific substitution rates across multiple complete genomes. Genome Res, 17(12):1932–1942, Dec 2007.

    [7] C.E.V. Storm and E.L.L. Sonnhammer. Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics, 18(1):92–99, Jan 2002.

    [8] Hollich V., Milchert L., Arvestad L., and Sonnhammer E. Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction. Mol Biol Evol, 22:2257–2264, 2005.

    [9] Wapinski, I. A. Pfeffer, N. Friedman, and A. Regev. Automatic genome-wide reconstruction of phyloge- netic gene trees. Bioinformatics, 23(13):i549–i558, 2007.


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