Closed clydeandforth closed 4 years ago
Hi James,
Yes you can do this with BactDating. When you run the bactdate command you will need to fix the substitution rate using the arguments "initMu=mu,updateMu=F". The value mu you set it to should be expressed for the whole 6 genes alignment, not per site. If you know the clock rate per site, you should multiply this by the sum of the lengths of the 6 genes to get the correct value of mu. You will also need to use the argument "date=rep(N,2019)" where N is your number of genomes, to specify that all genomes have the same date.
Best wishes, Xavier
Hi James,
Yes you can do this with BactDating. When you run the bactdate command you will need to fix the substitution rate using the arguments "initMu=mu,updateMu=F". The value mu you set it to should be expressed for the whole 6 genes alignment, not per site. If you know the clock rate per site, you should multiply this by the sum of the lengths of the 6 genes to get the correct value of mu. You will also need to use the argument "date=rep(N,2019)" where N is your number of genomes, to specify that all genomes have the same date.
Best wishes, Xavier
Is date=rep(2019,N)?
Yes well spotted it should indeed have been rep(2019,N)
Hi Xavier,
Can BactDating be used to infer divergence time at the species level if no temporal sampling data is available? I have a maximum likelihood species tree based on 6 housekeeping genes from a bacterial spatial sampling survey. Can I input the estimated substitution rate at the 6 loci to estimate when the species diverged?
Thanks,
James