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How FigTree calculates "Node Ages" node labels? #166

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AlesBucek opened this issue Feb 12, 2021 · 1 comment
Open

How FigTree calculates "Node Ages" node labels? #166

AlesBucek opened this issue Feb 12, 2021 · 1 comment

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@AlesBucek
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Hi!
I imported nexus-formatted tree into FigTre v1.4.4. When I display the "Node Ages" node label information, the value does not match any of the node information in the nexus file.

Example of one node:
Node information from nexus file:
[&CAheight_95%_HPD={0.0,49.72305407126764},
CAheight_mean=40.71613581558492,
CAheight_median=44.80661609279434,
CAheight_range={0.0,112.78985757784564},
height=44.856154673869845,
height_95%_HPD={39.43269073659225,51.151204474747715},
height_median=45.14262819035353,
height_range={22.355189445004555,61.710352533394385},
length=1.0307089196384953,
length_95%_HPD={0.39507621973169194,1.7725551732569897},
length_median=0.9760938200308402,
length_range={0.03298942551236905,6.471945221508747},
posterior=0.9608862197605007,
rate=0.005665744739773379,
rate_95%_HPD={0.003131605962014538,0.00849058288412562},
rate_median=0.00541913863162671,
rate_range={9.78434766709904E-4,0.06024127421570448}]

"Node Ages" node label from FigTree:
45,2401...

How is FigTree calculating the Node Ages? Is this a possible bug?
Thanks and cheers!
Ales

@aast242
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aast242 commented Jan 26, 2024

As far as I can tell, the Node Ages displayed in FigTree are identical to those returned by branching.times() in the R package ape (see documentation here), so I would assume they're calculated the same way.

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