Some really interesting things are going on in the alignment and phylogenetics world.
Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees
Kevin Liu,1 Sindhu Raghavan,1 Serita Nelesen,1 C. Randal Linder,2 Tandy Warnow1,*
Inferring an accurate evolutionary tree of life requires high-quality alignments of molecular sequence data sets from large numbers of species. However, this task is often difficult, slow, and idiosyncratic, especially when the sequences are highly diverged or include high rates of insertions and deletions (collectively known as indels). We present SATé (simultaneous alignment and tree estimation), an automated method to quickly and accurately estimate both DNA alignments and trees with the maximum likelihoodcriterion. In our study, it improved tree and alignment accuracy compared to the best two-phase methods currently available for data sets of up to 1000 sequences, showing that coestimation can be both rapid and accurate in phylogenetic studies.
1 Department of Computer Sciences, The University of Texas at Austin, One University Station C0500, Austin, TX 78712, USA.
2 Section of Integrative Biology, School of Biological Sciences, The University of Texas at Austin, One University Station C0930, Austin, TX 78712, USA.
I am excited to give this stuff a try on my largest alignments and take a look at the differences.
