I just read your recently published paper on OrthoClust approach. It is a well grounded work in both practically and mathematically point of views.
I ran your R scripts for my own data and It worked perfectly fine, however I am wondering how can I use the script for more than two species?
It could be appreciated if you help me to find the solution.
Thanks for your interest in OrthoClust. Orthoclust definitely works on more than 2. The R script is a primitive version for illustrating the concept outlined in the paper. We understand the importance of N-species generalization. We have put a new MATLAB code for N-species. It made use of an efficient code written by Mucha and Porter that implemented the Louvain algorithm for modularity optimization. The 3rd party code as well as our wrapper is now in the gersteinlab github.
Apart from MATLAB, we are planning to provide wrapper for Python or R later.
The N-species code is not exactly the thing we did for the paper. So if you find any bug or question, please let me know. we are trying to make a more user friendly package anyway.