NrdJm phylogeny

All NrdJm sequences from NCBI’s RefSeq database were downloaded from RNRdb (http://rnrdb.pfitmap.org) and clustered with USEARCH (Edgar 2010) at 90% sequence identity to reduce redundancy. Non full-length sequences and sequences of dubious quality were manually removed, before aligning all 363 sequences with ProbCons (Do et al. 2005). Trustworthy alignment positions were selected with the BMGE algorithm (Criscuolo and Gribaldo 2010) using the BLOSUM30 substitution matrix, ending up with 363 well-aligned positions forming 350 distinct alignment patterns. RAxML version 8.2.4 (Stamatakis 2014) was used to estimate a phylogeny, using the PROTGAMMAAUTO model, rapid bootstrapping with the autoMRE bootstopping followed by a full maximum likelihood tree search.The file is viewable with Dendroscope (Huson et al. 2007).v2: Addition of Lactobacillus leichmannii sequence.所有源自NCBI参考序列（RefSeq）数据库的NrdJm序列均从RNR数据库（RNRdb，http://rnrdb.pfitmap.org）下载，并通过USEARCH（Edgar 2010）以90%序列同一性完成聚类以降低数据冗余。在使用ProbCons（Do等人2005）对全部363条序列进行多序列比对前，手动剔除了非全长序列与质量存疑的序列。随后采用BMGE算法（Criscuolo与Gribaldo 2010）结合BLOSUM30替换矩阵筛选可靠的比对位点，最终得到363个比对质量优异的位点，共形成350种独特的比对模式。使用RAxML 8.2.4版本（Stamatakis 2014）进行系统发育树估算：选用PROTGAMMAAUTO模型，基于autoMRE自举停止准则开展快速自举检验，随后执行完整的最大似然树搜索。该结果文件可通过Dendroscope（Huson等人2007）查看。v2版本：新增莱氏乳杆菌（Lactobacillus leichmannii）序列。