Using R, the statistical analysis and computing platform, swapping two columns in a matrix is really easy:
m[ , c(1,2)] <- m[ , c(2,1)].
Note, however, that this does not swap the column names (if you have any) but only the values. You could do something like
colnames(m) <- colnames(m) if you need the names changed as well, but better is perhaps just to assign:
m <- m[ , c(2, 1, 3:ncol(m)) ]