PT  - JOURNAL ARTICLE
AU  - Lucas Czech
AU  - Alexandros Stamatakis
TI  - Methods for Automatic Reference Trees and Multilevel Phylogenetic Placement
AID  - 10.1101/299792
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 299792
4099  - http://biorxiv.org/content/early/2018/04/11/299792.short
4100  - http://biorxiv.org/content/early/2018/04/11/299792.full
AB  - 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 automatically construct representative sequences from databases to infer reference phylogenies. Second, we present an approach for conducting large-scale phylogenetic placements on nested phylogenies. Third, we describe a preprocessing pipeline that allows for handling huge sequence data sets. Our experiments on empirical data show that our methods substantially accelerate the workflow and yield highly accurate placement results.Implementation Freely available under GPLv3 at http://github.com/lczech/gappa.Contact lucas.czech{at}h-its.orgSupplementary Information Supplementary data are available at Bioinformatics online.