Does anyone know an online program that can generate a multiple sequence alignment and a consensus sequence?

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Biljana Arsic

I hope so that the following link will be helpful for you: http://blast.ncbi.nlm.nih.gov/Blast.cgi.

Please try also MOE software.

Danai-Stella Gkotsi

Between ClustalW and Muscle I suggest Muscle. It can align better different sequence lengths. Then MEME is nice for graphic representation of consensus. Check the URL bellow:

http://www.ebi.ac.uk/Tools/msa/muscle/

http://meme.nbcr.net/meme/cgi-bin/meme.cgi

Max Myakishev-Rempel

Can you recommend a DNA alignment program that can sort heterogeneous sequences into groups and produce multiple consensuses?

Leonardo Costa Fiorini

I tried to generate such consensus with 2 small interesting Java-written programs: Base-by-Base (https://4virology.net/virology-ca-tools/base-by-base) and Aliview (https://ormbunkar.se/aliview). None of them yielded a consensus the way I needed, as a single-letter code for nucleotides (explained in this website: https://www.bioinformatics.org/sms2/iupac.html). Even EMBOSS Cons failed to generate it, but as last I found one able to do so:

UGENE

https://ugene.net

As a plus, this program is free open-source. I really liked it and found it much better than BioEdit. I hope you like it too.

Aswin S Soman

If you want to do it online : Cons from EMBOSS : https://www.ebi.ac.uk/Tools/msa/emboss_cons/

If you want to do it commandline : muscle : For MSA & em_cons: For creating consensus