Hi Santiago,
This approach is implemented in phangorn, from ?optim.pml:
If the option 'optRooted' is set to TRUE than the edge lengths of
rooted tree are optimized. The tree has to be rooted and by now
ultrametric! Optimising rooted trees is generally much slower.
Cheers,
Does anyone know a maximum-likelihood implementation that uses molecular
sequences to optimizes node ages instead of branch lengths (ala Felsenstein
2008, p. 266)?
It sounds like nice idea for using in time calibrations.
Cheers,
Santiago
Santiago Claramunt
Associate Curator
Department of
