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bayesiancook / phylobayes

PhyloBayes: phylogenetic reconstruction using infinite mixtures (CAT and CAT-GTR) -- serial version (for MPI, see pbmpi.git)
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95% HPD Intervals #6

Open CRL-CHAR opened 1 year ago

CRL-CHAR commented 1 year ago

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 commented 1 year ago

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,