Already nice answers, here is my thoughts:
Following David's suggestions, I would suggest that you need to put in more thoughts before attempting to quantify the divergence between a given set of species. Getting evolutionary distance in scale of time using tools discussed may provide an abstract way of the diversity pattern based on the data you have. If you are new to phylogeny tree implementation, I strongly recommend a quick read of this article.
In a nutshell: From a bioinformatics perspective, if you are looking at a set of plant species to get a "pattern of divergence" based on a distance matrix. You need to define a dataset (for example sequence (protein, dna or rna) then follow a typical phylogeny analysis pipeline.
Select a reference sequence from each
species > BLAST > Alignment >
For phylogeny analysis you may either use tools discussed here or go with the classic tool Phylip. A typical workflow for Protein sequence using Phylip to generate a distance matrix which can be visualised using phylogeny visualization tools will be as follows.
alignment -> seqboot -> protdist ->
neighbor -> consense
This will give you an abstract way of divergence among the plant species based on the sequence.
If you just need to get an idea where your species of interest in the tree of life without the sequence based data you may use Timetree as suggested by Haibao.