Add option to use MAFFT for alignment instead of HMMer

[dustine32]

For the purpose of displaying the TreeGrafter alignment of the query sequence in the PANTHER tree viewer, we'll need an alignment that fits the same length as the MSA used in the viewer. We can use MAFFT for this and should add the functionality as an option:

1. Take the query sequence and use HMMer to find its family hit as usual. This step also produces the alignment that we currently then use in the RAxML step.
2. If the new MAFFT option is set, do not use the HMMer alignment from the previous step. Run MAFFT against the family and query sequence.
3. Run RAxML using the MAFFT alignment.

[dustine32]

MAFFT allows inputting a "constrained" alignment, i.e., the family PIR file

[thomaspd]

It's the --seed option, for "seed alignment". See the documentation at:
https://mafft.cbrc.jp/alignment/software/manual/manual.html