Re: [R-sig-phylo] Maximum likelihood time-scaling

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,

[R-sig-phylo] Not inferring homology within "absence" state in phylogenetic analysis

Dear all Maybe someone has some insight here... I am coming up against the problem, when it comes to phylogenetic analysis. Basically I want to conduct a parsimony (or other phylogenetic) analysis where "inapplicable" scores are treated as separate states *for each taxon* . I.e. I want to