Python构建系统发生树，以冠状病毒基因组序列为例（COVID-19，SARS，MERS，EBOLA），最大似然估计法（ML）

系统发生树

定义

系统发生树（phylogenetic tree）是表明被认为具有共同祖先的各物种相互间演化关系的树

分类

• 是否有根？
  - 有根树：具有方向的树
  - 无根树：没有方向，其中线段的两个演化方向都有可能
• 基因树和物种树

构建方法

计算的精度和时间均依次增大

• 非加权分组平均法：UPGAM（Unweighted pair group method with arithmetic mean）
• 矩阵法：邻接法 neighbor-joining (NJ)
• 简约法：最大简约法 maximum parsimony (MP)
• 似然法：最大似然法 maximum likelihood (ML)
• 后验概率法：贝叶斯法 Bayesian

用什么序列建树？

• 如果DNA序列两两间一致度大于70%，选用DNA序列
• 低于70%选用蛋白质序列或DNA序列

What is the difference between a guide tree and a true phylogenetic tree?

A guide tree is calculated based on the distance matrix that is generated from the pairwise scores. The output can be found in the .dnd file. A phylogenetic tree is calculated based on the multiple alignment that it receives. The distances between the sequences in the alignment are calculated and can be found in the .ph file. These distances are then used by the method chosen (nj, phylip, dist) to make the phylogenetic tree (.nj, .ph, .dst file).

from Bio import SeqIO

## 读入序列数据

covid = SeqIO.read('data/covid19.fasta', 'fasta')
sars = SeqIO.read('data/sars.fasta', 'fasta')
mers = SeqIO.read('data/mers.fasta', 'fasta')
ebola =