Dear Shinichi,
A fast solution is provided by the function chronoMPL in ape; it does
not require calibration points (see the references in the help page of
this function for the assumptions). The function chronos (also in ape)
is another possibility but it needs at least one calibration point
(though this can be fixed to unity at the root).
Note that a correlation matrix can be calculated from a non-ultrametric
tree: see the function vcv.
Best,
Emmanuel
Le 29/10/2016 à 05:26, Shinichi Nakagawa a écrit :
Dear List
We would like make several non-ultrametic trees (based on molecular data;
downloaded from treeBASE) into ultrametric trees using R. Could you advice
us what is the best and the most general way of doing this please?
We would like to use resultant ultrametric trees in phyologenetic
comparative analysis (by turning into correlation matrices).
Best wishes,
Shinichi Nakagawa
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