Alignments' consensuses alignment

Question

[Мики-рики-тави]

I've got 800 alignments, with from 2 to 80 sequences each. Is there any way to align the consensus sequences of each alignment. This operation is presented in the Geneious Prime but I need the license for it. Is there another way?

[lieven.sterck]

Hi Мики-рики-тави,

welcome to the forum.

I edited your title and removed the word 'URGENT' from it, and certainly the exclamation marks! Keep in mind that we are all volunteers here spending their, likely little, free time in helping out the community. If anyone has valuable input to provide to help resolve your issue, they will do so in due time.

Urging people to deal with your question will often have the opposite effect of what you hope to achieve.

[cpad0112]

If you already have alignment in standard formats such as fasta, msf, try programs like cons to extract conserved sequence/pattern from each alignment and run them through alignment software like muscle, t-coffee.

Answer 1

[Istvan Albert]

You may align the consensus sequences with multiple sequence alignment tools like Clustal Omega or MAFFT. That is probably the utility that Geneious implements as well. Read up in the documentation of what it actually does.

Export the consensus sequences into a single FASTA file and proceed with the software.