Calibration points missing node bars
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coyotree commented
Hello,
Followed the advice of several people here (#30) to calculate the error in node ages for a phylogeny. Briefly, I
- made 100 bootstrap trees from an alignment using RAxML
- ran RAxML on those bootstrap trees using a constraint to get branch lengths
- rerooted the resulting trees using the same outgroup (phyx)
- ran treePL prime, CV and the final smoothing run on all the trees found in a file
- Converted the resulting trees to NEXUS after inputting them into FigTree
- Summarized using TreeAnnotator
Now I have error bars around all nodes except where I placed calibration points (see image; nodes missing any error bar is where a calibration point was placed). The points themselves had minimum and maximum ages so one would expect there to be error bars around those nodes as well. I cannot figure out why this is happening.
Any advice appreciated.
coyotree commented
Sorry, this is NOT a treePL problem. Just realized there are ranges at those nodes but for some reason the bars do not show up. Sorry for the junk issue.