FixedTreeAnalysis - Node ages from ML Fixed Tree

[Álvaro Pita Ramírez]

Hello,

I'm trying to use BEAST 2.7 with the FixedTreeAnalysis package. The fixed tree is a Maximum Likelihood Tree in NEXUS format that I've made with IQ-Tree. This tree has Substitution per Site as branch lengths. When I try to set MRCA priors using fossil calibrations with Offsets for my sequences I get errors and P of -Infinity for these priors.

My question is, is it possible to get absolute node ages (in Millions of years) in a Fixed Tree analysis if the original fixed tree does not contain such dates in its nodes?

Thank you in advance :)

Álvaro

[Gustavo Ballen]

Hello,

The node ages need to be consistent with your node calibrations. Here's a vignette of our tbea R package showing how to do it https://gaballench.github.io/tbea/articles/starting_tree.html

Although the example used a parsimony tree from TNT, you can skip that part and focus on how to do with your ML tree.

Best wishes,

Gustavo

Gustavo A. Ballen, PhD.

FAPESP Postdoctoral Fellow

Instituto de Biociências - Câmpus de Botucatu

Universidade Estadual Paulista "Júlio de Mesquita Filho"

Botucatu, SP, Brazil

https://github.com/gaballench

https://gaballench.com/

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