This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Multiple Alignment (~1400 sequences)

Hello,

I need to align some sequences from a virus. The virus has 7 serotypes, and I got about 200 sequences of each sorotype. I have to determine the identity between the sequences of the same sorotype, and to find out the phylogeny between the sorotypes.

What is the best way to align the sequences in each of this situations?

muscle sequence multiple-alignment mafft
• 2,664 views • link
updated by Ram Ram • written by l.souza l.souza

Are the sequences from different genes? Whole viral genomes?

• 0 views • link
written by h.mon h.mon

They are the whole viral genome

• 0 views • link
written by l.souza l.souza

1 answer

Assuming you have thousands of somewhat related assembled virus genomes, you should:

  1. align them with MAFFT.
  2. reconstruct phylogeny with RAxML or ExaML.
• 0 views • link
written by h.mon h.mon

Is there an specific reason to use RAxML or ExaML?

• 0 views • link
written by l.souza l.souza

They are fast and deal easily with large datasets. There are other software available though, I recommended two I've worked before.

• 0 views • link
written by h.mon h.mon

Ok. Thank you so much! Can't wait to try it...

• 0 views • link
written by l.souza l.souza

Is there any similar option to RAxML that allows me define other substition model than GTR family?

• 0 views • link
written by l.souza l.souza

Long time since I used it, but I think for DNA only GTR or CAT (a fast approximation to GTR, for large datasets). There are more option for protein models.

• 0 views • link
written by h.mon h.mon

I've already solved it... I'm gonna use GTR with a gamma correction!

Thank you, even so!

• 0 views • link
written by l.souza l.souza

Log in to answer this question.

More posts like this