Analysing tree topologies

[Flo89]

Hi guys,

In my current work I am working on phylogenetic tree reconstruction for big datasets. At a later stage I will compare the tree topologies of "my" reconstructed trees against topologies of a published paper.

I would like to use a method or tool to obtain possible differences in the tree topologies.


Are there any open source tools available to solve this question ? Or do you have other suggestions ?

Thanks !!!

Best,
Flo89

[Richard Finney]

This is a good question. I hope we get some discussion.
I too have the problem of a ("phyloeseque") network of subclones using mutated genes from Exome and amp/dels network from low coverage WGS; and have asked myself the question "are these tree like networks basically the same"? So ... is there an accepted method for comparing networks.

I do note this WGCNA package : https://labs.genetics.ucla.edu/horva...HumanBrain.pdf

Comparing with an image thought might be a problem; unless you can re-code into data comparable with your data.

[lskatz]

There are many comparison metrics. I have been looking into the Kendall-Colijn metric recently and am trying to port it to an Rscript at my github site. However, it is available as an R package and I believe a Shiny package at Michelle Kendall's site.

The metric itself is discussed in their 2015 paper.