Pangenome gene trees of 41 Pseudorhizobium and Neorhizobium strains

Gene trees were computed for each of the 6,714 homologous gene family of the 41-species pangenome with at least 4 sequences using MrBayes (Ronquist &amp; Huelsenbeck 2003) under the GTR+4G+I model, running the Metropolis-coupled Markov chain Monte-Carlo (MCMCMC) for 2,000,000 generations, sampling a tree every 500 generations. Convergence of bipartition distribution in independent pairs of 4,000 sampled gene tree sets (‘chains’) was achieved for all gene families under these conditions.<br>Only the consensus of these tree chains (discarding the first 25% sampled trees as burn-in) are presented here.Correspondance of gene family and coding sequence identifiers with metadata (genome of origin, genome location, functional annotation, etc.) is available using the Pantagruel database provided in the related post (open with SQLite 3).

针对41物种泛基因组（pangenome）中6714个各含至少4条序列的同源基因家族（homologous gene family），我们采用MrBayes软件（Ronquist与Huelsenbeck，2003），基于GTR+4G+I模型，运行马尔可夫耦合马尔可夫链蒙特卡洛（Metropolis-coupled Markov chain Monte-Carlo，缩写MCMCMC）算法，执行200万代迭代，每500代采样一次基因树（gene tree）。在该参数配置下，所有基因家族的4000组独立采样基因树集（即“链”）的二分分支分布均已收敛。
本文仅展示上述基因树链的共识树，其中已将前25%的采样树作为预烧样本（burn-in）予以舍弃。基因家族与编码序列标识符及其元数据（来源基因组、基因组位置、功能注释等）的对应关系，可通过相关帖子中提供的Pantagruel数据库获取，该数据库可使用SQLite 3打开。