Methods for automatic reference trees and multilevel phylogenetic placement

Bioinformatics
Lucas CzechAlexandros Stamatakis

Abstract

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. 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 datasets. Our experiments on empirical data show that our methods substantially accelerate the workflow and yield highly accurate placement results. Freely available under GPLv3 at http://github.com/lczech/g...Continue Reading

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Citations

Feb 6, 2020·Bioinformatics·Lucas CzechAlexandros Stamatakis
Feb 27, 2020·Molecular Biology and Evolution·Mandev S GillGuy Baele
Jan 8, 2020·GigaScience·Andreas BremgesAlice C McHardy
Jul 9, 2020·Bioinformatics·Connor Morgan-LangSteven J Hallam
Nov 1, 2020·Nature Communications·Joran MartijnThijs J G Ettema
Apr 29, 2020·Journal of Oral Microbiology·Noriaki SatoYasushi Okuno
Aug 21, 2020·FEMS Microbiology Ecology·S S BotnenP B Eidesen
Nov 7, 2020·The Journal of Eukaryotic Microbiology·Marc GottschlingMicah Dunthorn
Dec 15, 2020·Molecular Biology and Evolution·Benoit MorelAlexandros Stamatakis
Apr 28, 2021·Molecular Ecology Resources·Jose S HleapMelania E Cristescu

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Methods Mentioned

BETA
PCA

Software Mentioned

RAxML
Sativa
ng
EPA
Phylogenetic Automatic ( Reference ) Tree ( PhAT
pplacer
hmmalign
PhATs
Silva
PaPaRa

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