Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution

Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB

Volumn 8, Issue , 2004, Pages 326-335

  Arvestad, Lars ^a   Berglund, Ann Charlotte ^b   Lagergren, Jens ^a   Sennblad, Bengt ^c  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^b STOCKHOLM UNIVERSITY   (Sweden)

^c KAROLINSKA INSTITUTE   (Sweden)

Author keywords

Algorithms; Bayesian analysis; Gene tree; Orthology; Reconciliation

Indexed keywords

ALGORITHMS; COMPUTATIONAL METHODS; GENETIC ENGINEERING; INTEGRATION; MONTE CARLO METHODS; PROBLEM SOLVING; TREES (MATHEMATICS);

BAYESIAN ANALYSIS; GENE TREE; ORTHOLOGY; RECONCILIATION;

GENES;

EID: 2442562450     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/974614.974657     Document Type: Conference Paper

References (15)

1. U. Arnason and A. Janke. Mitogenomic analyses of eutherian relationships. Cytogenetic and Genome Research, 96(1-4):20-32, 2002.
2. L. Arvestad, A.-C. Berglund, J. Lagergren, and B. Sennblad. Bayesian gene/species tree reconciliation and orthology analysis using MCMC, Bioinformatics/ISMB'03,19:i7-il5, 2003.
3. J. Felsenstein. Evolutionary trees from DNA-sequences - a maximum-likelihood approach. Journal of Molecular Evolution, 17(6)1368-376, 1981.
4. W. M. Fitch. Distinguishing homologous from analogous proteins. Systematic Zoology, 19(2):99-113., 1970.
5. W. R. Gilks, S. Richardson, and D. J. Spiegelhalter, editors. Markov Chain Monte Carlo in Practice. Chapman and Hall, 1996.
6. W. Hoeffding. Probability inequalities for sums of bounded random variables. Journal of the American Statistical Association, 58(301 ):13-30, Mar. 1963.
7. J. P. Huelsenbeck and F. Ronquist. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17(8):754-755, Aug 2001.
8. T. Jukes and C. Cantor. Evolution of protein molecules. In H. Munro, editor, Mammalian protein metabolism, pages 21-132. Academic Press, New York, 1969.
9. D. G. Kendall. On the generalized "birth-and-death" process. Annals of mathematical statistics, 19:1-15, 1948.
10. C. Lanave, G. Preparata, and C. Saccone. Mammalian genes as molecular clocks? Journal of Molecular Evolution, 21(4):346-50, 1984.
11. M. Nei, X. Gu, and T. Sitnikova. Evolution by the birth-and-death process in multigene families of vertebrate immune system. Proceedings of the National Academy of Science, USA, 94(15):7799-7806, July 1997.
12. F. Rodriguez, J. L. Oliver, A. Marin, and J. R. Medina. The general stochastic model of nucleotide substitution. Journal of Theoretical Biology, 142(4):485-501, 1990.
13. U. Swenson, A. Backlund, S. McLoughlin, and R. S. Hill. Nothofagus biogeography revisited with special emphasis on the enigmatic distribution of subgenus Brassospora in New Caledonia. Cladistics, 17(1):28-47, 2001.
14. D. L. Swofford, G. J. Olsen, P. J. Waddell, and D. M. Hillis. Phylogenetic inference. In D. M. Hillis, C. Moritz, and B. K. Mable, editors, Molecular systematics, pages 407-514. Sinauer Associates Inc., Sunderland, MA, 2nd edition, 1996.
15. J. L. Thorne, H. Kishino, and I. S. Painter. Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution, 15(12):1647-1657, 1998.