Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer.

ABSTRACT: Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at t

SUBMITTER: Bromberg R 

PROVIDER: S-EPMC4918981 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature