Invariant sites for snp tree?

[Tonny-zhou]

Hi! Thank you for BactDating.

I' am a newcomer to the phylogenetic filed. I find that the output of the substitution rate from BactDating for the tree based on only the snp sites is large than those previously reported (for the strain staphylococcus aureus). I want to know whether it is due to lacking the invariant sites?

Thank you

[xavierdidelot]

Hi Tonny,

Yes indeed if your tree was built using SNPs only then you should rescale the branches of this tree before running BactDating. To rescale you can use something like: tree$edge.length=tree$edge.length*L where L is the genome length and tree is the tree based on SNPs with branch lengths measured per site.

[Tonny-zhou]

Hi Tonny,

Yes indeed if your tree was built using SNPs only then you should rescale the branches of this tree before running BactDating. To rescale you can use something like: tree$edge.length=tree$edge.length*L where L is the genome length and tree is the tree based on SNPs with branch lengths measured per site.

Does the genome length include the invariant sites?

[xavierdidelot]

Yes by "genome length" I mean the length of the whole genome including invariant sites.