Do you want to quantify or visualize incongruence of the trees?

I have maximum likelihood trees which I had build their MLST and complete genome tree. There are differences in their clustering even though its the same sample. Other than raw eye analysis, I would like to use software to proof their differences too.

I hope these may help you

https://www.researchgate.net/post/What_is_the_best_methodology_to_compare_the_phylogenetic_tree_probability_of_Bayesian_InferenceBI

Thanks for the information Ahmad El-banhaway. Will give it a try.

There are several ways to demonstrate that the two tree topologies differ. These include consensus techniques, tree distance measures, and tree-by-tree comparisons. I use TNT (Goloboff et al. 2008) and Dendroscope (Huson and Scornavacca 2012) to either quantify or visualize the differences between trees. TNT can build consensus trees (strict, semi-strict, majority rule, and frequency difference consensus) and calculate tree distances (SPR and Robinson-Foulds distances). SPR distance tells you how many subtree prune-and-regraft moves away is one tree from another (a simple and intuitive similarity measure). TNT can also build so called “anticonsenus” tree (“tcomp;” command) by showing groups present in one tree but not in another (and vice versa). Dendroscope can build so called “tanglegram” to visualize the differences between trees. In tanglegram, two trees are depicted with their tips facing each other and corresponding terminal taxa are connected by lines. It can also calculate several types of distance measures not implemented in TNT. There is a plenty of techniques for measuring and testing incongruence in phylogenies. Here is a useful review to start with:

http://www.sciencedirect.com/science/article/pii/S153204640500081X

Ohhh very useful piece of information for a new learner like me. Thanks Pavel Duda.

use Dendroscope software