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General Category >> Bugs and Issues >> Problem: Sequences have different alphabets https://forum.ugene.net/forum/YaBB.pl?num=1266248471 Message started by pablo on Feb 15th, 2010 at 10:41pm |
Title: Problem: Sequences have different alphabets Post by pablo on Feb 15th, 2010 at 10:41pm
Hi,
thank you for this great editor. I wish to align app. 30000 sequences using muscle 4.0 algorithm integrated into the ugene editor. I got the error message "Sequences have different alphabets" after clicking on export to Clustal. Do you have any advice for me? Thanks. |
Title: Re: Problem: Sequences have different alphabets Post by Mikhail Fursov on Feb 16th, 2010 at 8:27pm
Hi Pablo,
This error means that your alignment contains sequences of different alphabets, for example both nucleic and amino, or contains some symbols UGENE doesn't know how to process (we call this 'raw' alphabet) In this case its impossible to make an alignment since you can't assign scores to match operation. UGENE reports error when you try to create such files. However I think that there is a good chance here for improvement from our side. Could you attach the alignment so we can analyze the error in details? BTW, I would not suggest using Muscle 4 today as mainstream version of the alignment algorithm. Muscle 3 is significantly faster and more stable. Muscle 4 is just an preview release. BTW2, Note that starting from version 1.6.1 UGENE contains KAlign algorithm. We recommend using it for a huge number of sequences (~100k) when Muscle becomes too slow to do the job |
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