Sat, 26 Jul 2008 06:25:33 BST CiteULike: dpollard's Huelsenbeck http://www.citeulike.org/user/dpollard/author/Huelsenbeck CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/dpollard/article/2288308 <i>Science, Vol. 319, No. 5862. (25 January 2008), pp. 473-476.</i><br /><br />The statistical methods applied to the analysis of genomic data do not account for uncertainty in the sequence alignment. Indeed, the alignment is treated as an observation, and all of the subsequent inferences depend on the alignment being correct. This may not have been too problematic for many phylogenetic studies, in which the gene is carefully chosen for, among other things, ease of alignment. However, in a comparative genomics study, the same statistical methods are applied repeatedly on thousands of genes, many of which will be difficult to align. Using genomic data from seven yeast species, we show that uncertainty in the alignment can lead to several problems, including different alignment methods resulting in different conclusions. 10.1126/science.1151532 Alignment Uncertainty and Genomic Analysis Karen Wong Marc Suchard John Huelsenbeck doi:10.1126/science.1151532 Science, Vol. 319, No. 5862. (25 January 2008), pp. 473-476. 2008-01-25T07:09:02-00:00 2008 Science 319 5862 473 476 alignment alignment_accuracy