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xavierdidelot / BactDating

Bayesian inference of ancestral dates on bacterial phylogenetic trees
https://xavierdidelot.github.io/BactDating
MIT License
81 stars 15 forks source link

ML tree to coalescent tree #6

Closed mushalallam closed 5 years ago

mushalallam commented 5 years ago

Hi, can I import a maximum likelihood tree to BactDating? or convert it to coalescent tree ? Thanks in advance Mushal

xavierdidelot commented 5 years ago

Yes a ML tree computer for example using raxml or phyml is a perfectly valid input. The only thing to be careful about is that branch lengths need to be measured in units of substitutions, not substitutions per site. You can often achieve this simply by multiplying all branch lengths with the number of sites L in your genomes, for example in R using something like: tree$edge.length=tree$edge.length*L If you forget to do this there should be a warning in BactDating to remind you.