Bucky for tree comparison from nuclear vs mito

[Inbar Maayan]

Hi Cécile

I'm new to bucky, and was wondering whether it's possible to use Bucky to determine what 

proportion of loci yield a tree that matches the topology of a second tree.

In my case, I ran two sequencing experiments for the same set of individuals, one for 

ddrad and one for mito sequences, with the goal of comparing the resulting trees.

Now, I have a tree generated from ddrad-seq data, and a tree generated from 

mitochondrial data (both using SNPs) for the same set of individuals -- is there 

a way to use bucky to compare the two types of trees, or to ask what proportion of 

gene trees in the ddrad species tree match the mito species tree? They are quite discordant 

so this would be a useful thing to know. 

If I have misunderstood and Bucky is not the right tool for the job, that would also be

very nice to know.

thank you kindly, Inbar

[Cécile Ané]

Based on your description, it looks like you need a different analysis than BUCKy, indeed.