如何利用ete3包从系统发育树中提取子树
ete3：用于构建、比较、注释、操作和可视化系统发育树的Python包。
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| conda install ete3 #conda安装
python #在操作文件目录下进入python命令行交互界面
import ete3 #导入ete3包
t = ete3.Tree("tree.txt") #将原来的进化树定义为t
subtree_taxa = ["Orbicella_annularis","Pocillipora_damicornis","Stylophora_pistillata","Hydra_vulgaris","Acropora_digitifera","Acropora_millepora","Acropora_tenuis","Porites_lutea","Renilla_muelleri","Discosoma_santahelenae","Amplexidiscus_fenestrafer","Dendronephthya_sinaiensis","Nematostella_vectensis","Exaiptasia_pallida","Actinia_equina"] #将待提取的物种列表存入subtree_taxa变量
t.prune(subtree_taxa,preserve_branch_length=True) #利用prune方法提取子树
print(t) #查看子树拓扑
t.write(outfile="subtree.txt") #将子树存为文件
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