BioPython中系统发育树的子树

Question

我有一个newick格式的系统发育树。我想根据终端节点的标签拉出一个子树(因此基于物种列表)。我正在使用的树的副本可以在这里找到：http://hgdownload.soe.ucsc.edu/goldenPath/dm6/multiz27way/dm6.27way.nh

目前，我已经使用BioPython读入了树，如下所示：

from Bio import Phylo
#read in Phylogenetic Tree
tree = Phylo.read('dm6.27way.nh', 'newick')
#list of species of interest
species_list = ['dm6', 'droSim1', 'droSec1', 'droYak3', 'droEre2', 'droBia2', 'droSuz1', 'droAna3', 'droBip2', 'droEug2', 'droEle2', 'droKik2', 'droTak2', 'droRho2', 'droFic2']

我如何才能拉出species_list中只有物种的子树呢？

Answer 1

好的，假设您想要包含物种列表中所有物种的最小树，您希望此树的根节点是列表中所有物种的最新公共祖先(MRCA)，谢天谢地，这已经在Phylo中实现了：

from Bio import Phylo

#read in Phylogenetic Tree
tree = Phylo.read('dm6.27way.nh', 'newick')
#list of species of interest
species_list = ['dm6',
                'droSim1',
                'droSec1',
                'droYak3',
                'droEre2',
                'droBia2',
                'droSuz1',
                'droAna3',
                'droBip2',
                'droEug2',
                'droEle2',
                'droKik2',
                'droTak2',
                'droRho2',
                'droFic2']

common_ancestor = tree.common_ancestor(species_list)
Phylo.draw_ascii(common_ancestor)

输出：

Clade
                                           ___ dm6
                                       ___|
                                      |   | , droSim1
                                      |   |_|
                            __________|     | droSec1
                           |          |
                           |          |  _____ droYak3
                          ,|          |_|
                          ||            |____ droEre2
                          ||
                          ||      _______ droBia2
                          ||_____|
                          |      |_____ droSuz1
                          |
                        __|                                  _______ droAna3
                       |  |_________________________________|
                       |  |                                 |________ droBip2
                       |  |
                       |  |___________________ droEug2
                       |
                       |_____________ droEle2
                      ,|
                      ||______________________________ droKik2
                    __||
                   |  ||______________ droTak2
___________________|  |
                   |  |____________ droRho2
                   |
                   |_______________ droFic2

Answer 2

使用ete3而不是BioPython。

from ete3 import Tree
t = Tree('dm6.27way.nh')
t.prune(species_list, preserve_branch_length=True)
t.write()

从文档中，

从版本2.2开始，此函数还包括preserve_branch_length标志，该标志允许从树中删除节点，同时保持剩余节点之间的原始距离。