NrdBik phylogeny
type: Dataset
description: Maximum likelihood phylogeny of NrdBk and NrdBi class I ribonucleotide reductase radical generating subunits. Sequences from NCBI's RefSeq database (Haft et al. 2018; https://doi.org/10.1093/nar/gkx1068), downloaded July 2018, was searched with subclass specific HMMER (Eddy 2011; https://doi.org/10.1371/journal.pcbi.1002195) profiles from RNRdb (http://rnrdb.pfitmap.org) representing the NrdBk and NrdBi subclasses plus an outgroup consisting of NrdBe and NrdBn. The choice of outgroup was made by analysis of the full NrdB phylogeny presented in Grinberg et al. 2018 (https://doi.org/10.7554/eLife.31529). The resulting sequences were clustered at 70% identity with UCLUST (Edgar 2010; https://doi.org/10.1093/bioinformatics/btq461) to create a representative set of sequences. After manual inspection of sequences, 144 out of 7725 original sequences remained. The sequences were aligned with ProbCons (Do et al. 2005; https://doi.org/10.1101/gr.2821705) and 158 reliably aligned positions were selected with BMGE (Criscuolo & Gribaldo 2010; https://doi.org/10.1186/1471-2148-10-210) using the BLOSUM30 matrix. The alignment file is NrdBik_with_NrdBen.uc0.70.c.pb.BLOSUM30.bmge.alnfaa. A maximum likelihood phylogeny was estimated using RAxML v. 8.2.4 (Stamatakis 2014; https://doi.org/10.1093/bioinformatics/btu033) with the PROTGAMMAAUTO model using the rapid bootstopping algorithm and subsequent maximum likelihood search. The phylogeny, in Dendroscope (Huson et al. 2007; https://doi.org/10.1186/1471-2105-8-460) nexml format, is NrdBik_with_NrdBen.uc0.70.c.pb.BLOSUM30.bmge.PROTGAMMAAUTO.raxml.bipartitions.nexml.
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Daniel Lundin
date modified: 2019-07-01
date published: 2019-07-01
keywords: Evolutionary Biology
  type: DefinedTerm
  term code: 10615
keywords: Bioinformatics and Computational Biology
  type: DefinedTerm
  term code: 10610
keywords: 60102 Bioinformatics
keywords: 60309 Phylogeny and Comparative Analysis
license: https://creativecommons.org/licenses/by/4.0/
publisher: Stockholm University
version: 0

PropertyValue
property ID: DOI
value: 10.17045/STHLMUNI.8386652

Daniel Lundin
type: Person

Stockholm University
type: Organization