Multiple Alignment (~1400 sequences)

Question

[l.souza]

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?

[h.mon]

Are the sequences from different genes? Whole viral genomes?

[l.souza]

They are the whole viral genome

Answer 1

[h.mon]

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

1. align them with MAFFT.
2. reconstruct phylogeny with RAxML or ExaML.

[l.souza]

Is there an specific reason to use RAxML or ExaML?

[h.mon]

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

[l.souza]

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

[l.souza]

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

[h.mon]

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.

[l.souza]

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

Thank you, even so!