Bayesian NrdA phylogeny

Bayesian phylogeny of NrdA, class I ribonucleotide reductase catalytic component. Sequences from NCBI's RefSeq and Genbank databases (Haft et al. 2018; https://doi.org/10.1093/nar/gkx1068Opens in a new tab), downloaded March 2019, was searched with subclass specific HMMER (Eddy 2011; https://doi.org/10.1371/journal.pcbi.1002195Opens in a new tab) profiles for NrdA and NrdJ, class II RNR, serving as outgroup, (Lundin et al. in preparation). The resulting sequences were clustered at 60% identity with UCLUST (Edgar 2010; https://doi.org/10.1093/bioinformatics/btq461Opens in a new tab) to create a representative set of sequences. After manual inspection of sequences, 342 out of 27821 original NrdA sequences remained, plus 26 NrdJ sequences selected for aligning well to NrdA. The sequences were aligned with ProbCons (Do et al. 2005; https://doi.org/10.1101/gr.2821705Opens in a new tab) and 283 reliably aligned positions were selected with BMGE (Criscuolo & Gribaldo 2010; https://doi.org/10.1186/1471-2148-10-210Opens in a new tab) using the BLOSUM30 matrix. The alignment file is NrdA_uc0.60.NrdJ_uc0.30_outgroup.intr.correct.nolb.co.profile.BLOSUM30.bmge.mb.nxs. A bayesian phylogeny was estimated with MrBayes v. 3.2.6 (Ronquist & Huelsenbeck 2003; https://doi.org/10.1093/bioinformatics/btg180Opens in a new tab; https://github.com/NBISweden/MrBayesOpens in a new tab) using a gamma distribution for rate variation and rjMCMC to jump between amino acid models. MrBayes was run with four chains and five runs until average standard deviation of split frequencies reached 0.015. (See NrdA_uc0.60.NrdJ_uc0.30_outgroup.intr.correct.nolb.co.profile.BLOSUM30.bmge.mb.) The phylogeny, in Dendroscope (Huson et al. 2007; https://doi.org/10.1186/1471-2105-8-460Opens in a new tab) nexml format, isNrdA_uc0.60.NrdJ_uc0.30_outgroup.intr.correct.nolb.co.profile.BLOSUM30.bmge.mb.con.fullname.nexml .