Multiple Sequence Alignment for >20 Sequences

Question

[griffinwhy]

I'm trying to align 319 variants of the rabies virus to see which regions are more highly conserved. However, all of the multiple sequence alignment tools I've found cap out at 20 sequences. Is there one I haven't considered/is there a way to string together a bunch of sequence alignments?

[GenoMax]

Are you referring to online/web based tools? When used on the command line none of the tools should have that limit. If you need something based on a GUI then take a look at MEGA.

[Brice Sarver]

Are you aligning alignments or constructing MSAs from batches of genes/genomes? What's your input size?

Answer 1

[piet]

My preferred multi sequence aligner for the command line is mafft nowadays. The rabies virus has a genome size about 12000 nt. It should be feasible to align > 20 whole genomes with mafft on an standard PC, maybe within 10 minutes or less.