How to dealign MSAs? Or how best to merge MSAs?

Question

[jbt38]

I have ten MSAs per gene for a group of organisms, that I need to merge (e.g. 10x cytB, 10x COI...). How can I dealign these MSAs for realignment together? Alternatively, is there a way to "merge" multiple MSAs into one?

[GenoMax]

You could export the fasta files from the alignments (don't do aligned fasta if you don't want to have gaps etc). Or use something like MEGA to see if you can read the alignments in and then re-do a larger one combining multiple.

[jbt38]

Thanks, but what do you mean? I do not have access to the pre-aligned fastas, only the 10x10 MSAs. What I would like to do is just dealign all of them (i.e. all CytB, all COI...) and then align them with Mafft.

[GenoMax]

You will have to explain 10x10 MSA (I am not familiar with that term)? You don't have the aligned data in a standard MSA alignment format (MSF, ALN or some such)?

[jbt38]

Sorry, yes they are MSA files in fasta format, which are previously aligned. There are 10 alignments of 10 loci (e.g. 10 for COI, 10 for CytB, 10 for each of the others).

[GenoMax]

Then you should be able to simply read them into various programs and go from there. If that does not work then simply export as fasta and then read back in.

[jbt38]

Thanks, the issue is I thought that alignment programs such as Mafft require unaligned sequences. In which case I should think about dealigning them, which Is what I'm looking for advice about. I think I should dealign them, put them into one file and align them.

[GenoMax]

You could use a program like MEGA and do this via a GUI on your local desktop i.e. conversion to plain fasta.

You could also remove non-ACTG characters using UNIX tools like sed which will make them into plain multi-fasta fies.