Methods for automatic reference trees and multilevel phylogenetic placement.

ABSTRACT:

Motivation

In most metagenomic sequencing studies, the initial analysis step consists in assessing the evolutionary provenance of the sequences. Phylogenetic (or Evolutionary) Placement methods can be employed to determine the evolutionary position of sequences with respect to a given reference phylogeny. These placement methods do however face certain limitations: The manual selection of reference sequences is labor-intensive; the computational effort to infer reference phylogenies is substantially larger than for methods that rely on sequence similarity; the number of taxa in the reference phylogeny should be small enough to allow for visually inspecting the results.

Results

We present algorithms to overcome the above limitations. First, we introduce a method to automatica

SUBMITTER: Czech L 

PROVIDER: S-EPMC6449752 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature