Update MantelTest_withinTreeDistances.r

halved the number of calculations by changing script from:
for (i in 1:length(matrix_list)) {
    for (j in 1:length(matrix_list)) {

to:
for (i in 1:length(matrix_list)) {
    for (j in i:length(matrix_list)) {

Also, added the remove outgroup command from the cophenetic calculations (line 14)