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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.
Thanks,
Cody Coyotee
The text was updated successfully, but these errors were encountered:
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.
Hello,
Followed the advice of several people here (#30) to calculate the error in node ages for a phylogeny. Briefly, I
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.
Thanks,
Cody Coyotee
The text was updated successfully, but these errors were encountered: