I would like to calculate the phylogenetic distance between 500 patients' breast cancer subtypes and need help when it comes to the right method for producing distance matrices. My patients are equally divided between the 5 sub-types (100 each) and the number of variables represents the number of possible mutated genes and the number of mutations found. Here's an example
LuminalA LuminalB HER2 TNBC BRCA1 15 45 16 8 KRAS 17 28 6 3 BRAF 19 8 32 28 BCN1 9 15 27 54
I'm currently considering one of PHYLIP's components but I'm open to more viable solutions, so any advice on how to handle the issue is welcome.