演講公告
新聞標題： ( 2013-03-14 )
演講主題：Influence of Alignment Uncertainty on Homology and Phylogenetic Modeling
主講人：張家銘先生 (Centre for Genomic Regulation, Barcelona, Spain)
演講日期：2013年04月01日 11:10-12:00
演講地點：交通大學(光復校區)綜合一館427室
茶會時間：上午10:50-11:10於交大統計所428室舉行
摘要內容：
Most evolutionary analyses are based upon pre-estimated multiple sequence alignment models.From a computational point of view, it is as complex to estimate a correct alignment, as it is to derive a correct tree from that alignment. Several works have recently reported on the influence of multiple sequence alignment on downstream analysis, and on the uncertainty inherent to their estimation (Talavera, Castresana 2007; Markova-Raina, Petrov 2011; Jordan, Goldman 2012). We will discuss about the causes of alignment ambiguities, which can be classified in two categories: external or internal. External uncertainties are related to methodology and the different algorithms used for the alignment process while internal ones are less trivial and result from the variation of the input data. Wong et al. established the external uncertainty that multiple alignment procedures induce when reconstructing phylogenies (Wong, Suchard, Huelsenbeck 2008). They were able to show that in many cases different aligners produce different phylogenies, with no simple objective criterion sufficient to distinguish among hese alternatives. The lack of internal robustness of MSA methods is well illustrated in the recent Heads-or-Tails methodology, where it has been shown that substantial variation can occur when estimating an MSA on a set of sequences and subsequently on the same sequences reversed from left to right (Landan, Graur 2007). A more generic sampling can be done that would involve breaking all ties arbitrarily, as done in the GUIDANCE bootstrap strategy (Penn et al. 2010). However, this approach is computational intensive due to bootstrap procedure and requires a substantial code modification in most MSA packages. I will describe how I addressed those two kinds of alignment uncertainties. We show that a weighted sampling external alignment uncertainty for helping subsequent phylogenetic analysis. A reliability measure by transitive consistency score for handling internal uncertainty is proposed.
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