Several methods have been developed to   construct phylogenetic trees. In general these methods can be divided into   two distinct classes: methods which use an optimality criterion to choose a   tree or trees, and methods that use an algorithm to choose a tree.

Optimality criterion: Accomplishes the   goal of estimating a phylogeny by defining criteria for comparing alternative   phylogenies to one another and deciding which tree is better, or that more   than one are equally good. Ideally, the simplest approach to find the best   tree(s) would be to evaluate every possible tree and choose the best one   based on your criterion. Felsentstein (1978) calculated the number of   possible rooted, bifurcating trees for specific numbers of terminal taxa.   Based on these calculations it can be seen that the number of possible trees   for a fairly low number of taxa soon becomes quite large.

目前，已发展出几种构建系统发生树的方法。一般来说，这些方法可以分为两类：使用最优性准则筛选树的方法和使用算法筛选树的方法。

最优性标准：通过定义比较不同系统发育树的标准，并决定哪一棵树（或哪些树）更好，从而实现估计系统发育的目标。理想情况下，找到最佳树的最简单方法是评估每个可能的树，并根据既定标准选择最优树。Felsentstein（1978）计算了特定数量终端分类群下可能的有根分叉树的数量。根据这些计算，可以看出，即使基于相当低数量的分类群，可能的系统发育树很快就会变得相当大。