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NrdJ phylogeny

dataset
posted on 29.07.2020, 10:57 by Daniel Lundin
Maximum likelihood phylogeny (RAxML; Stamatakis 2014) of representatives of 75% identity USEARCH clusters (Edgar 2010) of the full diversity of class II ribonucleotide reductases (NrdJ). Reliable positions in a Probcons (Do et al. 2005) alignment were selected with the BMGE algorithm using the BLOSUM30 matrix (Criscuolo & Gribaldo 2010) PROTGAMMAAUTO model.

The alignment is available in Seaview format (Gouy et al. 2010; http://doua.prabi.fr/software/seaview) with defined character sets for the different BMGE selections. The phylogenetic tree is available in nexml format that can be opened in Dendroscope (Huson et al. 2007; http://dendroscope.org/) and other tree viewers.

Funding

Swedish Research Council Grant 2016–01920

Swedish Cancer Society Grant CAN 2016/670

History

Associated Publication

Loderer et al., 2017 (Journal of Biological Chemistry 292, 19044-19054). https://doi.org/10.1074/jbc.M117.806331

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