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Old 09-06-2018, 01:07 AM   #1
kajsa
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Location: Uppsala, Sweden

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

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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Old 09-13-2018, 03:17 AM   #2
colindaven
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Muscle might be good. MUGSY is probably excellent for this use case given the length of the sequence.

cheers
Colin
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Old 09-13-2018, 04:13 AM   #3
kajsa
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Quote:
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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