Trying to give a short resume of what i did:
1 - From a metgenomics illumina 2x150 bp I have cleaned reads and assembled reads into contigs. For each contig i have done gene prediction and extracted bacterial marker genes (based on Campbell et All paper).
2- With bacterial markers genes i have predicted proteins and assigned taxonomy using kaiju (actually diamond or blast will work as well).
3. So i end up building an abundance table for all my samples (normalized table in RPM).
Now, i would like to compare samples. In 16S i used to work with uifrac distances matrices. The problem here is that i only have the distance matrix so i was wondering what would be the best approach ??
I was thinking of using the ape package a compute a distance matrix of my abudance table but i would like advice.