How long does it take muscle to do an alignment ? I have about 500 sequences with length 30000 and it has been running for four days! is that normal!
It is normal. No regular alignment program is meant for sequences that are 30000 long. They usually deal better with large number of relatively short sequences, and the only way to accommodate long sequences is usually if they are >95% identical.
If your sequences are highly identical, you may have luck with this option. Also see these tips. Searching Biostars may uncover other clues as well.
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version 2.3.6
Thank you for these info.