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NBISweden / MrBayes

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:
http://NBISweden.github.io/MrBayes/
GNU General Public License v3.0
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To obtain absolute dates (from current date) #235

Open Alexei-Kassian opened 3 years ago

Alexei-Kassian commented 3 years ago

By default MrBayes reports dates for internal nodes and the root counted from the date of the most recent taxon. That is the zero on the timeline coincides with the date of the most recent taxon. This is not the problem in the case of a dataset with extant taxa.

But I work with a dataset which only contains fossils (of various ages). E.g. the most recent taxon is dated back to 500 kya. For a certain internal node, MrB infers the date 1000 kya. Actually it means that the node is dated back to 1500 kya BP.

Is it possible to get a tre-file with absolute dates, i.e., dates counted from the current date? In other words how to obtain the date 1500 kya for a node in the example above?

Alexei-Kassian commented 3 years ago

As s palliative solution I introduced an additional artificial extant taxon as an outgroup:

Extant 0000000... calibrate Extant = fixed(0); constraint ingroup = 2-.; prset topologypr=constraints(ingroup);

It doesn't work properly, however, since such an outgroup changes absolute dates and statistical support for the 'ingroup' taxa.