Calculating genome similarity between viruses

[Zongzhi Wu]

Can I get viral genome similarity in Output Files? Thanks~

[Zongzhi Wu]

And how can I generate a phylogenetic tree by utilizing the output of vcontact2.0?

[Ben Bolduc]

Regarding the phylogenetic tree, unfortunately, this isn’t something that vContact2 can provide. What you could do - if you had a large enough VC, is take the members of a VC and run a phylogenetic tool using genomes/proteins from them.

For genome similarity, vContact2 doesn’t use “similarity” in the traditional context. You can get the gene-to-gene similarity from the Diamond output, or you could get the similarity “scores” from the network file. These scores are the -log of the probability that any two genomes are sharing genes by chance. So, if two genomes share 99 of their 100 genes, it’s really, really unlikely that they’re unrelated. That gets converted to a large positive value (let’s say 250) and becomes the edge weight for the network that is used for clustering.

Adding a phylogenetic component would be great for the next version of vContact2!

[Ben Bolduc]

Closing due to feature not being in vConTACT2, nor planned. The next version this might be a possibility...