串联法建树

Current microbial taxonomies based on 16S rRNA gene relationships3,6,7,8 have several limitations, including low phylogenetic resolution at the highest and lowest taxonomic ranks14, missing diversity as a result of primer mismatches15 and PCR-produced chimeric sequences that can corrupt tree topologies by drawing together disparate groups16. Trees inferred from the concatenation of single-copy vertically inherited proteins provide higher resolution than those obtained from a single phylogenetic-marker gene17,18,19 and are increasingly representative of microbial diversity, as culture-independent techniques are now producing thousands of metagenome-assembled genomes (MAGs) from diverse microbial communities20,21,22. Despite some caveats of their own, including potential lateral gene transfer, differing rates of evolution, and recombination19,23, ***concatenated protein trees have been extensively used in the literature20,24,25 and have been proposed as the best basis for a reference bacterial phylogeny***26.

from: https://www.nature.com/articles/nbt.4229

我们这里将以不同物种之间保守的单拷贝核基因为基础，分别运用串联法(Concatenation)（先将不同物种之间的每个单拷贝基因单独进行多序列比对，然后将这些比对后的单拷贝基因进行首尾相连串接成一个supergene矩阵，最后将这个supergene用于构建系统发育树）和并联法(Coalescence)（先将不同物种之间的每个单拷贝基因单独进行多序列比对，并构建每一个单拷贝基因对应的基因树，然后将所有单拷贝基因对应的基因树进行合并重构出相应的物种树）进行ML系统发育树的构建。

题目：如何轻松构建物种系统发育树
作者：Davey1220
链接：https://www.jianshu.com/p/bfa568c8f4c4
来源：简书
这篇文章有构建的方法

此外，

2021,NBT也有相关的建树内容可以参考。