Count: Evolutionary analysis of phylogenetic profiles with parsimony and likelihood

Bioinformatics

Volumn 26, Issue 15, 2010, Pages 1910-1912

  Csurös, Miklós ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGY; COMPUTER PROGRAM; METHODOLOGY; PHYLOGENY; PROBABILITY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; PHYLOGENY; PROBABILITY; SOFTWARE;

EID: 77955038643     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq315     Document Type: Article

References (20)

1. Alexeyenko,A. et al. (2006) Automatic clustering of orthologs and inparalogs shared by multiple genomes. Bioinformatics, 22, e9-e15.
2. Arvestad,L. et al. (2004) Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. In Gusfield,D. (ed.) RECOMB '04: Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology.ACM, NewYork, NY, pp. 326-335.
3. Arvestad,L. et al. (2009) The gene evolution model and computing its associated probabilities. J. ACM, 56,7.
4. Caetano-Anollés,G. (2005) Evolution of genome size in the grasses. Crop Science, 45, 1809-1816.
5. Csu{double acute}rös,M. (2008) Ancestral reconstruction by asymmetric Wagner parsimony over continuous characters and squared parsimony over distributions. In Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop. Vol. 5267 of Springer Lecture Notes in Bioinformatics, Heidelberg, pp. 72-86.
6. Csu{double acute}rös,M. and Miklós,I. (2006) A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer. In Proceedings of the Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB). Vol. 3909 of Springer Lecture Notes in Bioinformatics, Heidelberg, pp. 206-220.
7. Csu{double acute}rös,M. and Miklós,I. (2009) Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model. Mol. Biol. Evol., 26, 2087-2095.
8. Farris,J.S. (1970) Methods for computing Wagner trees. Syst. Zool., 19, 83-92.
9. Farris,J.S. (1977) Phylogenetic analysis under Dollo's law. Syst. Zool., 26, 77-88.
10. Felsenstein,J. (1973) Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst. Zool., 22, 240-249.
11. Fitch,W.M. (2000) Homology a personal view on some of the problems. Trends Genet., 16, 227-231.
12. Kendall,D.G. (1949) Stochastic processes and population growth. J. R. Stat. Soc. B, 11, 230-282.
13. Koonin,E.V. and Galperin,M.Y. (2002) Sequence-Evolution-Function: Computational Approaches in Comparative Genomics. Kluwer Academic Publishers, New York.
14. Krylov,D.M. et al. (2003) Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res., 13, 2229-2235.
15. Nei,M. and Rooney,A.P. (2005) Concerted and birth-and-death evolution of multigene families. Ann. Rev. Genet., 39, 121-152.
16. Pagel,M. (1999) Inferring the historical patterns of biological evolution. Nature, 401, 877-884.
17. Pellegrini,M. et al. (1999)Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA, 96, 4285-4288.
18. Tatusov,R.L. et al. (1997) A genomic perspective on protein families. Science, 278, 631-637.
19. Witmer,P.D. et al. (2003) The development of a highly informative mouse simple sequence length polymorphism (SSLP) marker set and construction of a mouse family tree using parsimony analysis. Genome Res., 13, 485-491.
20. Yutin,N. et al. (2009) Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. Virol. J., 6, 223.