Hi!

I notice that multiple sequence alignment(clustalw, muscle, kalign) in ugene starts with aln files instead of fasta file. Meaning users have to generate *aln file first and then run MSA. Why is it designed that way?

Perhaps ugene dev should looke into bioedit to compare how both perform MSA or as a bioinformatics tool in general.

Yep, you are correct.

When you work with UGENE visual interface FASTA is opened as a set of sequences, but not as alignment. The only way to show FASTA content as alignment is to convert it (1 click in UGENE) to alignment format (sto, aln...). This is fundamental limitation of the V1.x data model of UGENE.

If you work with Workflow Designer - there are no such limitation and you can read alignments from FASTA easily.

In UGENE 2.0 this limitation is removed and you will be able to read alignments from FASTA or from any other format with sequences if needed without extra conversion step.