how to show the branch lengths by using Figtree

[Jenny]

Hi,

I have a question from the reviewer that 'the MCC tree should not end all at the same line', then how to show different length of branch other than ultrametric tree. We have used the strict clock as the model. Many thanks!

Best,

Jenny

[Patrice Showers Corneli]

Do a run without the strict clock (which forces the branches to evolve at the same rate across the tree), note the likelihood score and compare it to the strict clock tree likelihood. If the likelihood for the relaxed tree is better than your data does not fit a strict tree (very little data fits a strict clock - ultrametric assumptions almost always fail).

Patrice Showers Corneli
Associate Research Professor
Department of Biology
University of Utah 
Salt Lake City, UT 84112
cor...@biology.utah.edu

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[Santiago Sánchez]

Hi Jenny,

There are two ways, that I know of, to show branch lengths in an ultrametric tree using FigTree: 1) select the "length" parameter in the branch label tab; this way show branch lengths numerically; and 2) use a color gradient to color branches according to their length.

I think the reviewer's question is a bit weird. The only thing that can lead to tips not being aligned at the end is heterocronous sampling (time-stamp calibration. e.g. incorporate the sampling times of each terminal into the model). If you didn't do this, there is no reason why all tips "should not end at the same line". Maybe I'm misunderstanding.

Cheers,

Santiago

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Santiago Sanchez-Ramirez, PhD

Postdoctoral Associate

Ecology and Evolutionary Biology

University of Toronto

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