Compare whole genomes

Question

[Vero_virus]

Hi everyone,

I'm focus on virus evolution. I want to determine the genetic component(s), gene o genes that explain a morphologic characteristic of some virus variants. I created two phylogenetically related databases. Can anyone suggest any software to compare whole genomes? I need to identify the gene(s) or nucleotide variant responsible for a phenotype.

Thanks

[GenoMax]

You can either use nextstrain suite of apps or specifically augur to do phylogenomics of viruses ( see https://github.com/nextstrain )