Hi! Are you talking about Sanger reads?
Quote:I'm doing it with the align short sequences tools and options by default
Short reads are next-generation sequencing data. There are usually thousand or even millions of them to be aligned. So this is not the right choice for your type of data.
Quote:Is this the best way to do this??
It is better open the sequences in the Alignment Editor. As you have a reference sequence, add it also to the sequence alignment. Then, you can do pairwise alignment of each sequence with the reference. And also do some additional manual aligning.
If you like, I can show you the procedure in more details in a webinar.
Note, that we're going to improve this procedure in UGENE 1.16.
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