95% HPD Intervals

[CRL-CHAR]

How does one extract the 95% HPD intervals using Phylobayes? Is there a command for these to be calculated? It does not seem like they are included in the .chronogram file.

I am using Phylobayes 4.1c

[bayesiancook]

Hi,

the readdiv command should give you all this information:

readdiv -x chainname

the .chronogram file contains the 95% credible intervals as branch support values (as: lowerage_upperage); the .dates file also contains them, tabulated across all nodes (columns 4 and 5), although you then have to match those lines with the node labels / indices (which are given in the .labels file).

does that help ?

best,