subfunction split_seq deals more robustly with splitting strings longer than the maximum regex
Handle using mafft as an alternate aligner.
convert spaces to underscores in the names of fasta sequences
switch to using split_seq instead of a regex
Align the ends of the contig seqs to the reference seq by trimming or padding.
Merge pull request #84 from juliema/mafft-integration

Mafft integration