What is the best program for MSA of 33 very similar sequences 113 00 bp long?

kajsa

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What is the best program for MSA of 33 very similar sequences 113 00 bp long?

09-06-2018, 01:07 AM

Hello,

I want to do a multiple sequence alignment with 33 sequences that are 99,99% similar and are around 113000 bp long.

I have looked around and found MAFFT and MAUVE. Are there any other programs to use that I've missed?

Thankful for any advise.
Kajsa
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colindaven

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09-13-2018, 03:17 AM

Muscle might be good. MUGSY is probably excellent for this use case given the length of the sequence.

cheers
Colin
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kajsa

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09-13-2018, 04:13 AM

Originally posted by colindaven View Post

Muscle might be good. MUGSY is probably excellent for this use case given the length of the sequence.

cheers
Colin

Thanks a lot!
Kajsa
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What is the best program for MSA of 33 very similar sequences 113 00 bp long?

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