I'm trying to correlate results of tree comparison with properties of the genomes in trees.
Trees were built from distance matrices obtained with FastANI and "my" k-mer based method. My method was employed with several values of parameter t controlling degree of finding homologous genes in a very primitive manner.
I'm using PHYLIP, neighbor joining and UPGMA methods were used to built the trees, branch score distance and symmetric difference to compare them. I was comparing FastANI matrices with each of t values for my method.
Now I want to figure out the possible connection between received results in a combination of k-mer length/t value/build method/compare method and used dataset.
How can I examine genome properties except for ANI/genetic distance? Any ideas?