Distance matrix based on mutation rates

Question

[ceruleanivy]

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.

Answer 1

[Charles Yin]

You may use Pearson coefficient of the distance matrix.