Analyse diversity in nucleotide sequences of one gene

Question

[khhgng]

I have a fasta format file with sequences of one gene from 1000 Arabidopsis accessions.

What would be the best way to cluster and visualise these sequences on basis of SNPs among them ?

Many thanks

[GenoMax]

Multiple sequence alignment using t-coffee, MAFFT, muscle.

[khhgng]

Thanks. So in that case what's a better approach for making a tree considering very high sequence similarity - Neighbour joining or parsimony or ...?

[GenoMax]

Depends on what you want to do. If you only want to visualize the SNP's then you don't need to make a tree.

[khhgng]

I would rather want to cluster them based on SNPs. That may bring more sense to the evolutionary part regarding this one locus.

[GenoMax]

And that may automatically happen. Run the MSA and then you could edit it (within reason) to show what you want to demonstrate.

[Joe]

If your alignment is good/close it probably won't make a difference what method you use.