The most common way to create an alignment object is by using Bio::SimpleAlign (see also Bio::Align::AlignI). These are the objects that Bio::AlignIO (mostly) creates as output. If you have some non-standard alignment format, parse it using Perl and generate Bio::LocatableSeq objects. Then feed those to the Bio::SimpleAlign using
Note: the Bio::SimpleAlign object represents alignments, it does not create alignments. Here we assume you already have your sequences aligned in some (more or less) sane format or other. To generate alignments see...