Neisseria core genome alignment and phylogeny

All publicly available genomes from the <i>Neisseria </i>genus were downloaded from NCBI (as of December 30, 2017) and annotated with Prokka v 1.12. <i>N. gonorrhoeae </i>and <i>N. meningitidis </i>were subsampled to 20 genomes. Core genes (n = 236) were identified and aligned with Roary v 3.12.0. Approximate maximum likelihood phylogenetic analysis was performed used FastTree v 2.1.9. The phylogeny was visualized using FigTree (http://tree.bio.ed.ac.uk/software/figtree/). Branches are scaled by substitutions per site.

截至2017年12月30日，从美国国家生物技术信息中心（NCBI）下载所有公开可用的奈瑟菌属（Neisseria）基因组序列，并使用Prokka v1.12完成注释。将淋病奈瑟菌（N. gonorrhoeae）与脑膜炎奈瑟菌（N. meningitidis）的基因组样本抽降至20个。鉴定得到236个核心基因（n=236），使用Roary v3.12.0进行多序列比对。采用FastTree v2.1.9开展近似最大似然系统发育分析。使用FigTree（http://tree.bio.ed.ac.uk/software/figtree/）对系统发育树进行可视化。分支长度按每位点的碱基替换数进行缩放。