Question: Multiple Sequence Alignment for >20 Sequences
0
gravatar for griffinwhy
11 months ago by
griffinwhy0
griffinwhy0 wrote:

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?

alignment sequence • 306 views
ADD COMMENTlink modified 10 months ago by piet1.7k • written 11 months ago by griffinwhy0

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.

ADD REPLYlink modified 11 months ago • written 11 months ago by genomax83k

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

ADD REPLYlink written 11 months ago by Brice Sarver3.5k
1
gravatar for piet
10 months ago by
piet1.7k
planet earth
piet1.7k wrote:

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.

ADD COMMENTlink modified 10 months ago • written 10 months ago by piet1.7k
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