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rcedgar / muscle

Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.
https://drive5.com/muscle
GNU General Public License v3.0
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Memory Object Too Large due to very long sequences #63

Closed bioinfonerd closed 1 year ago

bioinfonerd commented 1 year ago

Love working with muscle, but I have a current alignment issue. I want to compile a consensus sequence from 11 sequences that are ~2,500,000 in length. Computer resources are not an issue, but seems max memory allowed is 215Mb. Is there a way I can change this?

rcedgar commented 1 year ago

This is because the sequences are MUCH too long for muscle (or any other MSA program I know of). Sequences this long have re-arrangement events and therefore do not have global alignments. The practical limit on sequence length in the current muscle is very roughly 20k letters.

bioinfonerd commented 1 year ago

Thank you for the response