NrdJ phylogeny

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.

针对全部第二类核糖核苷酸还原酶（class II ribonucleotide reductases, NrdJ）的全谱系多样性序列，选取其75%序列同一性的USEARCH聚类簇（Edgar 2010）的代表序列，采用RAxML软件（Stamatakis 2014）构建最大似然系统发育树。在Probcons（Do等人，2005）生成的多序列比对结果中，基于BLOSUM30矩阵（Criscuolo & Gribaldo 2010）并结合PROTGAMMAAUTO模型，通过BMGE算法筛选出可靠的比对位点。
该多序列比对结果以Seaview格式（Gouy等人，2010；http://doua.prabi.fr/software/seaview）提供，其中包含针对不同BMGE筛选结果的自定义字符集。本研究构建的系统发育树以nexml格式存储，可通过Dendroscope（Huson等人，2007；http://dendroscope.org/）及其他树状结构可视化工具打开查看。