I need to run a Incongruence Length Difference Test (ILD) also called the Partition Homogeneity Test. I have very little command line experience and I am on a pretty tight deadline. I've been using MEGA and Geneious with the PAUP plugin for most of my work and it's been going fine except for this. I have 4 likelihood trees that I would like to combine for a multi-locus sequence analysis but I think an ILD would be required to make this a viable phylogeny. All loci have positive dN/dS ratios below one. I would be welcome to any other ideas on how to show that they are appropriate to concatenate. Thanks!