Hi,

I am actually quite a newbie in bioinformatics/molecular biology, so probably my question is kind of a silly one. I have been using ClustalX2 for some time and adding of sequences to be aligned is very easy there. In UGENE, however, I am almost lost... Say, I have several FASTA sequence files that I can feed to ClustalX2 to do an alignment without any problems. In UGENE, what I can do with these files is only to open and to view the sequence (well, and analyze them, but one at a time). The only way to do an alignment that I have found so far is to export one sequence as alignment and then, in the open Alignment Editor window, add more sequences to the list and finally to align them all using one of the methods. Did I miss anything and there is an easier way to do alignments?
I do not find the way to switch to the Alignment Editor window in the newly created project with several open sequences... Is it the way it should be and I need to export at least one sequence as alignment to be able to actually do alignments?
Sorry if the question sounds stupid, but the way I am using UGENE seems to me quite weird...
P.S. The manual doesn't say anything about switching into the Alignment Editor.
P.P.S. I am using 1.10.4 under WinXP.
Thank you.

Well, the export of sequences is the correct way to perform the alignment from FASTA files which contain only one sequence.  It is written in manual:
http://ugene.unipro.ru/documentation/manual/plugins/dna_export/seq_as_alignment.html
http://ugene.unipro.ru/documentation/manual/alignment_editor/working_with_alignment/align_sequences.html

The conversion (export to alignment) is required because sequence object and alignment object have different representations and provide different features. If you try opening a multi FASTA file, UGENE would ask how to interpret it: as an alignment or as separate sequence objects.

However, if you u would like to automate alignment process I suggest you to use the Workflow Designer. I have attached an example schema which reads provided sequences, creates alignment representation from them and performs alignment, all in one turn.

You can read more about Workflow Designer here:
http://ugene.unipro.ru/documentation/wd_manual/index.html

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Konstantin Okonechnikov wrote on Apr 23^rd, 2012 at 12:43am:

Well, the export of sequences is the correct way to perform the alignment from FASTA files which contain only one sequence.  It is written in manual

Thank you very much for the explanations. I was just not sure if I was doing it the right way.