Add mafft as alternative to muscle

[iimog]

Thanks for the quick response. Can you also please add an mafft option? I tried a 1200 genome collection and the alignment is slow if using muscle. I think this will be very easy to implement and we can use more threads for alignment.

Thanks,

Jianshu

Originally posted by @jianshu93 in https://github.com/molbiodiv/bcgTree/issues/42#issuecomment-707974415