一、进化树构建之前，要对DNA的核苷酸序列或者同源蛋白质分子的氨基酸序列进行序列比对。
序列比对软件包括：
1.Clustalw
2.MAFFT
3.MUSCLE
二、构建进化树利用的统计模型：
1，maximum likelihood------------final likelihood values
2，bayesian inference
3，maximum parsimony
4，neighbor joining
The computation of large phylogenetic trees with statistical models such as maximum likelihood or bayesian inference is computationally extremely intensive. It has repeatedly been demonstrated that these models are able to recover the true tree or a tree which is topologically closer to the true tree more frequently than less elaborate methods such as parsimony or neighbor joining.
进化树构建方法准确性比较
================ML tree 相关===============
文章“Evolutionary Treesfrom DNA Sequences: A Maximum Likelihood Approach”
文章网址：http://xueshu.baidu.com/usercenter/paper/show?paperid=2ca6b67a1f95e2646e9e1fc400409517&site=xueshu_se
一篇ML构树原理的文章，还没有读。
三、核苷酸替代模型
JC69 、K80 、F81、TN93，HKY和GTR 模型
p-距离模型
Jukes-Cantor 模型
Kimura两参数模型
核苷酸替代模型的选择 - IQ-tree(ModelFinder) - 知乎 (zhihu.com)
四、进化树构建软件
IQ-TREE
https://doi.org/10.1093/molbev/msu300
参考：
