MSA: Difficulties in Multiple Sequence Alignment for virus

Question

[stars_point]

I'm not sure whether others face same problem with me. I am trying to align my 100++ of virus sequences through MAFFT, CLUSTALW. None of them give me expected result (create lots of gaps, align at wrong location,etc),perhaps T-Coffee give a better result but it does not work for large entries and time consuming.

Well most of the time I edit my alignment myself from the output of MAFFT, same again it takes time for large entries and not efficient.

I am wonder any of you have encountered same problem with me and how do you guys solve it? Or any recommendation in MSA tools which might help in this kind of situation.

Thanks =D

Answer 1

[wpwupingwp]

mafft --globalpair

Answer 2

[Mohamed]

I used clustal omega

And then I download the output file from the result page and used it in Jalview

Hope I am correct.

Best wishes, Mohamed

Answer 3

[oweitu]

I ran my analysis through the analysis pipeline developed at Montpellier Lab,

MSA default is MUSCLE, alignment curation and trimming by Gblocks, Phylogeny by PhyML and tree rendering by TreeDyn.

One can customise which algorithm suits one if these are not satisfactory.

Cheers!