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<mailto: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.<http://www.rom.on.ca/vikings> Christian Dior<http://www.rom.on.ca/dior> Wildlife Photographer of the Year<http://www.rom.on.ca/wpy> Here We Are Here: Contemporary African Canadian Art<http://www.rom.on.ca/en/exhibitions-galleries/exhibitions/here-we-are-here-black-canadian-contemporary- 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<http://www.rom.on.ca/fr/vikings> Christian Dior<http://www.rom.on.ca/fr/dior> Le Photographe naturaliste de l'année<https://www.rom.on.ca/fr/photographe-naturaliste> Nous Sommes Ici, D'ici : L'art Contemporain des Noirs Canadiens<https://www.rom.on.ca/fr/expositions-et-galeries/expositions/nous-sommes- ici-dici-lart-contemporain-des-noirs-canadiens> À VENIR 2 juin | Iris van Herpen : Transformer la mode 16 juin | Les araignŽes [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
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