Creates a copy of an MSA sequence
an MSA object
If m is stored in R (as it is by default), then m2 <- copy.msa(m1) is no different than m2 <- m1. But if it is stored as a pointer to a C structure, this is the only way to make an explicit copy of the MSA object.
an MSA object which can be modified independently from the original object
Melissa J. Hubisz and Adam Siepel