Hello,

I am trying to align two Sanger reads I received. I have imported the chromatograms to the Ugene software and exported the sequence with .aln format.

However, when I select both sequences and click on align with Muscle I get the following error message:

[22:55:13] 'MUSCLE align 'pcDNA4.aln'' task failed: Subtask {Workflow wrapper 'MUSCLE align 'pcDNA4.aln''} is failed: Subtask {Run workflow: align} is failed: Internal error: cannot find workflow alig

I am not very familiar with all features of the software, I have mainly been using ugene to check for chromatogram quality and do in silico cloning.
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I am using Windows 10 and have downloaded the latest version as a standard package.

I would be grateful if you could help me with this issue,
Thanks,
Can

Hello, Can.

MUSCLE is used for multiple sequence alignment that is global. It may be better to use some feature in UGENE that does local alignment. For example:

• Export only one sequence as an alignment.
  
• Select the second sequence object in the Project View.
  
• Click "Align sequence to this alignment" in the Alignment Editor.
  

Another option, for example, is to map both sequences to a reference, if you have it.

Also, you should use either the recommended online installer package or the full package as they contain external tools out of the box.

If you send us the sequences, I may check the issue and give you more exact guidelines.