EvolBioInf/phylonium

Defining the total number of substitutions

Closed this issue · 4 comments

goodolgab commented

Hi!

I'm currently working on a dataset of 1000+ E. coli genomes.
Is there a way to find out the number of total sites used by Phylonium when it estimates the number of substitutions per site?

Thanks!

kloetzl commented

Apologies, I was on vacation. There is a the option -p that will list the segregating sites. Alternatively you can use -v to get the coverage which when multiplied with the length and mutation rate with give you the absolute number of mutations. Hope this helps.

goodolgab commented

No worries!
And thanks for the reply! Just to clarify, when you mention length, do you mean the branch lengths (i.e. estimated no. of substitutions), or the length of the reference genome?

kloetzl commented

I'm thinking along this line: genome length * portion covered * substitution rate = number of substitutions.

goodolgab commented

This makes a lot of sense! Thank you!