If FALSE, disregard the order of columns in the combined
MSA.
pointer.only
(Advanced use only, for very large MSA objects) If
TRUE, return object will be a pointer to an object stored in C.
Value
An object of type MSA
Details
If the MSAs do not contain the same set of sequences, the sequences
will be added to each MSA and filled with missing data. The order
of sequences is taken from the first MSA, and sequences are added to
this as necessary.