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Clustalw 2 - i cannot upload the fasta sequence file?!!

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Clustalw 2 - i cannot upload the fasta sequence file?!!

Postby gonulInScience » Tue Dec 08, 2009 2:31 pm

I want to do a very simple protein sequence alignment, however I cannot upload the fasta sequence file to the program. Command is:
Enter the sequence file name: XXX.txt
But after this command, again the main menu appears. It seems I'm doing something wrong, if anybody can help, I will appreciate:)
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Postby mith » Tue Dec 08, 2009 4:41 pm

get the offline version of clustalx, it has a gui so the interface should be more user friendly.
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Postby JackBean » Sat Dec 12, 2009 3:44 am

So, FASTA or *.txt? That's a little difference ;)
Do you have it in correct format? Can you attach the file here?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Postby qqsvery » Sat Dec 19, 2009 4:22 am

FASTA format is different from TXT format,please make sure you load the right format!
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Postby mith » Tue Dec 22, 2009 7:43 pm

txt isn't a format, it's just an extension.
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Re:

Postby JackBean » Tue Dec 22, 2009 8:31 pm

mith wrote:txt isn't a format, it's just an extension.

you can say that about anything... but the extension should tell you, what can you expect ;)
http://www.biolib.cz/en/main/

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Postby mfursov » Thu Dec 24, 2009 6:44 am

It will always be slow to perform tasks like alignment using free remote servers.
I would propose you running it locally.

BTW Clustal algorithm is quite slow. Check Muscle to get results of the same quality much faster.
You can download it here: http://www.drive5.com/muscle/download3.6.html
or here: http://ugene.unipro.ru you will find the same algorithm with a friendly interface and multi-core CPU optimizations.
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Postby fcs » Wed Aug 11, 2010 4:26 am

I agree with mfursov. MUSCLE is faster and will get you, at the least, the same quality alignment.

Here is a reliable server to run it on if you do not want the hassle of installing it locally:

http://www.ebi.ac.uk/Tools/muscle/index.html
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Postby gerry90 » Mon Aug 01, 2011 10:30 am

thank you for the last link it proved usefull for me either
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