The ability to map features exists in both MegAlign Pro and SeqNinja. Here are some reasons you might want to map features in one application versus the other:

If you want to: Use this application:
MegAlign Pro SeqNinja
View the alignment and the mapped features x
Configure alignment parameters x
Map features in an end-to-end alignment. For instance, to perform a Mauve alignment of end-to-end chromosomes with some rearrangement. x
Map VCF features from a .vcf file. x
Map features into a table, then edit the table before generating the resulting sequence or feature file x

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