Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

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Abstract
Rapid Tree Building: Phylogenetic reconstruction is used to determine the relationships between organisms and requires an accurate alignment and analysis of multiple sequences. Iterative rounds of alignment and tree building are often necessary to prevent errors in the phylogeny estimate. One such way to address this problem is to assess alignment and trees in a single step. However, efficient algorithms to analyze data sets of reasonable size have been lacking. Liu et al. (p. 1561 ; see the Perspective by Löytynoja and Goldman ) describe an iterative approach that simultaneously incorporates both alignment and phylogeny and applies a fast maximum likelihood algorithm to the tree-building part. By assembling the components of the methods in this way, accurate results were obtained for up to 1000 sequences. Thus, it is possible to produce coestimation of sequence alignment and phylogeny that is both rapid and accurate.