Phastand Rphast: Phylogenetic analysis with space/time models

Briefings in Bioinformatics

Volumn 12, Issue 1, 2011, Pages 41-51

  Hubisz, Melissa J ^a   Pollard, Katherine S ^b   Siepel, Adam ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Functional element identification; Statistical phylogenetics

Indexed keywords

ARTICLE; COMPUTER PROGRAM; GENETIC DATABASE; GENOME; GENOMICS; INFORMATION RETRIEVAL; INTERNET; METHODOLOGY; PHYLOGENY;

DATABASES, GENETIC; GENOME; GENOMICS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; PHYLOGENY; SOFTWARE;

EID: 79551634894     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbq072     Document Type: Article

References (29)

1. Margulies EH, Blanchette MNISC Comparative Sequencing Program, et al. Identification and Characterization of Multi-Species Conserved Sequences. Genome Res 2003;13:2507-18.
2. Cooper GM, Stone EA, Asimenos G, et al. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 2005;15:901-13.
3. Siepel A, Bejerano G, Pedersen JS, et al. Evolutionarily conserved elements in vertebrate insect, worm, and yeast genomes. Genome Res 2005;15:1034-50.
4. Guigó R, Dermitzakis ET, Agarwal P, et al. Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proc Natl Acad Sci USA 2003;100:1140-45.
5. Kellis M, Patterson N, Endrizzi M, et al. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003;423:241-54.
6. Siepel A, Diekhans M, Brejova B, et al. Targeted discovery of novel human exons by comparative genomics. Genome Res 2007;17:1763-73.
7. Pollard KS, Salama SR, Lambert N, et al. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 2006;443:167-72.
8. Prabhakar S, Noonan JP, Paabo S, et al. Accelerated evolution of conserved noncoding sequences in humans. Science 2006;314:786.
9. Kim SY, Pritcchard JK. Adaptive evolution of conserved noncoding elements in mammals. PLoS Genet 2007;3: 1572-86.
10. Moses AM, Chiang DY, Pollard DA, et al. MONKEY: identifying conserved transcriptionfactor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol 2004;5:R98.
11. Pedersen JS, Bejerano G, Siepel A, et al. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol 2006;2:e33.
12. Yang Z. A space-time process model for the evolution of DNA sequences. Genetics 1995;139:993-1005.
13. Rhead B, Karolchik D, Kuhn RM, et al. The UCSC Genome Browser database: update 2010. Nucleic Acids Res 2010;38:D613-9.
14. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 2007;24:l586-91.
15. Pond S, Muse S. HyPhy: hypothesis testing using phylogenies. In: Nielsen R, (ed). Statistical Methods in Molecular Evolution, Springer, 2005;125-81.
16. Kumar S, Nei M, Dudley J, et al. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinformatics 2008;9:299-306.
17. Asthana S, Roytberg M, Stamatoyannopoulos JA, et al. Analysis of sequence conservation at nucleotide resolution. PLoS Comput Biol 2007;3:e254.
18. Gross SS, Brent MR. Using multiple alignments to improve gene prediction. JComputBiol 2006;13:379-93.
19. R Development Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, 2010. http://www.R-project.org. ISBN 3-900051-07-0.
20. Siepel A, Haussler D. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol 2004;21:468-88.
21. Wang Y, Diehl A, Wu F, et al. Sequencing and comparative analysis of a conserved syntenic segment in the Solanacea. Genetics 2008;180:391-408.
22. Holloway AK, Begun DJ, Siepel A, et al. Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Res 2008;18:1592-601.
23. Pollard KS, Hubisz MJ, Rosenbloom KR, et al. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 2010;20:110-21.
24. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J RStat Soc B 1995;57:289-300.
25. Giardine B, Riemer C, Hardison RC, et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res 2005;15:1451-5.
26. Gentleman RC, Carey VJ, Bates DM, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004;5:R80.
27. Nakamura T, Aoki S, Kitajirma K, et al. Molecular cloning and characterization of Kremen, a novel kringle-containing transmembrane protein. Biochim Biophys Acta 2001;1518: 163-72.
28. Siepel A, Pollard K, Haussler D. New methods for detecting lineage-specific selection. In: Proceedings of the 10th International Conference on Research in Computational Molecular Biology. Berlin: Springer, 2006;190-205.
29. Siepel A, Haussler D. Computational identification of evolutionarily conserved exons. In: Proceedings of the 8th International Conference on Research in Computational Molecular Biology. New York, NY: ACM Press, 2004;177-86.