Bayesian coestimation of phylogeny and sequence alignment

Background: Two central problems in computational biology are the determination of the alignment and phylogeny of a set of biological sequences. The traditional approach to this problem is to first build a multiple alignment of these sequences, followed by a phylogenetic reconstruction step based on this multiple alignment. However, alignment and phylogenetic inference are fundamentally interdependent, and ignoring this fact leads to biased and overconfident estimations. Whether the main interest be in sequence alignment or phylogeny, a major goal of computational biology is the co-estimation of both. Results: We developed a fully Bayesian Markov chain Monte Carlo method for coestimating phylogeny and sequence alignment, under the Thorne-Kishino-Felsenstein model of substitution and single nucleotide insertion-deletion (indel) events. In our earlier work, we introduced a novel and efficient algorithm, termed the "indel peeling algorithm", which includes indels as phylogeneti...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Gerton Lunter, István Miklós, Alexei Drummond, Jens Ledet Jensen, Jotun Hein
• Keywords: BMCBI 2005, Computational Biology, Multiple Alignment, Sequence Alignment