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

[gonulInScience]

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:)

[mith]

get the offline version of clustalx, it has a gui so the interface should be more user friendly.

[JackBean]

So, FASTA or *.txt? That's a little difference
Do you have it in correct format? Can you attach the file here?

[qqsvery]

FASTA format is different from TXT format，please make sure you load the right format！

[mith]

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

[JackBean]

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

[mfursov]

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.

[fcs]

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

[gerry90]

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