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

[Emmanuel Paradis]

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,

Emmanuel

Le 08/02/2018 à 00:12, Santiago Claramunt a écrit :

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 Natural History
Royal Ontario Museum
100 Queen’s Park Crescent
Toronto, ON, M5S 2C6
CANADA

(416) 586-5520
sclaram...@rom.on.ca

&

Assistant Professor
Department of Ecology and Evolutionary Biology, University of Toronto












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

[Santiago Claramunt]

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 Natural History
Royal Ontario Museum
100 Queen’s Park Crescent
Toronto, ON, M5S 2C6
CANADA

(416) 586-5520
sclaram...@rom.on.ca

&

Assistant Professor
Department of Ecology and Evolutionary Biology, University of Toronto












ON NOW
VIKINGS: The Exhibition, presented by Raymond James 
Ltd.
Christian Dior
Wildlife Photographer of the Year
Here We Are Here: Contemporary African Canadian 
Art

COMING SOON
2 June | Iris van Herpen: Transforming Fashion
16 June | Spiders

À L’AFFICHE
VIKINGS : L'exposition, une présentation de Raymond James 
Ltée
Christian Dior
Le Photographe naturaliste de 
l'année
Nous Sommes Ici, D'ici : L'art Contemporain des Noirs 
Canadiens

À VENIR
2 juin | Iris van Herpen : Transformer la mode
16 juin | Les araignŽes

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