node labels figtree

[sara]

Hi all,

a question I posted long time ago and went unanswered... hope someone is listening now ;)

I have doubts on the meaning of all "node labels" possibilities in figtree (144)

Ran TreeAnnotator (262) for MCC tree with "node heights" as "median heights". when I check all values in Figtree, I have this (example of a node):

node age: -0.269

node height (raw): 0.269   # these match the node height in the figure

height: 0.288

height median = 0.252

I know these are small but why these differences, and what is exactly being calculated in each?

or any place I can see it?

In some cases/nodes differences are substantial. 

Plus, in the tree file (txt) one can only see height; height_median; height_HPD, height_range… (and same for rates and lengths).

Wondering if height (raw) and age are some internal things from figtree that may have some little bias… yet it is what is plotted

any help appretiatted,

many thanks in advance,

[Pavel Rinkman]

Hello, Sara!

This is a good question. I asked a similar one some time ago but have yet to get all answers. I can definitely say that the “raw“ height is the height you specified at the moment of the treeannotator launch: ca, mean, & median. The values specified as just length or height are confusing; they even do not coincide with the values of the MCC tree in the posterior. I have not checked the coincidence of height_median with “raw” values on -height median.

I hope that the answer shall be finally found!

Best wishes,
Pavel

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вторник, 25 апреля 2023 г. в 18:25:22 UTC+3, sara:

[Daniel Eusebio Quintero Vallejo]

Hello Sara, 

Did you manage to answer the question?

I have a similar problem :) Thank you!