Calibration

[Jaiane Oliveira]

Hi please someone help me. How do I estimate the divergence time using the BEAST v.2.7 program with calibrated dating with a cytochrome b (cytb) substitution rate of 2.1% per million years? Applying a normal distribution with a mean value of 0.0105 and a sigma of 0.0034 to the prior clock.rate of the cytochrome b (cytb) gene. This analysis is for a genus of birds.

[Omar Mejía]

You need to set the substitution rate in the clock model tab, after you run Beast you need to estimate the consensus tree and open with Figtree where you were able to see the divergence times in each node, there is a tutorial named taming the beast

https://taming-the-beast.org/tutorials/FBD-tutorial/

El dom, 24 mar 2024 a las 12:43, Jaiane Oliveira (<jjoj...@gmail.com>) escribió:

Hi please someone help me. How do I estimate the divergence time using the BEAST v.2.7 program with calibrated dating with a cytochrome b (cytb) substitution rate of 2.1% per million years? Applying a normal distribution with a mean value of 0.0105 and a sigma of 0.0034 to the prior clock.rate of the cytochrome b (cytb) gene. This analysis is for a genus of birds.

--
You received this message because you are subscribed to the Google Groups "beast-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to beast-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/beast-users/40ae3cc7-62b9-4f8f-9dea-26776e81da9an%40googlegroups.com.

--

Omar Mejía G

[Jaiane Oliveira]

Thank you very much for helping. I'll read the tutorial. Thank you.

To view this discussion on the web visit https://groups.google.com/d/msgid/beast-users/CAOEgSgnUirmc0FZ5nnKahhTOxhbjxHRTXtZDn%3DjXQaZTgjsF-A%40mail.gmail.com.

--

Jaiane Oliveira

Graduação em Ciências Biológicas UFMT

Mestranda no PPG Zoologia UFMT

Cuiabá-MT

Contato (66)99928-4246

[Carolina Gonzalez]

Hello, could you?
I still have doubts since I don't know where to put the substitution rate in a relaxed clock.

[Pedro Augusto Freire de Sá Pontes]

ORCrate

To view this discussion on the web visit https://groups.google.com/d/msgid/beast-users/a9a65757-2573-448b-9a55-40dbdee42aa4n%40googlegroups.com.

Enviado via UCSMail.

[Carolina Gonzalez]

Thank you very much but I get this Cannot invoke "beast.base.evolution.tree.Node.isRoot()" because "<parameter1>" is null. Do you know of any specific tutorial with a relaxed rate and clock?

Saludos

Dra. Carolina González , PhD

Investigador Postdoctoral, Instituto Milenio de Oceanografía

Celular :+56965791248

To view this discussion on the web visit https://groups.google.com/d/msgid/beast-users/CANZ9MMpA7YNdh5uY3dKJVOxwNfcW%3Dyez_UUjx7f9hAKJffkm6Q%40mail.gmail.com.

[Pedro Augusto Freire de Sá Pontes]

Sure! But I recommend you to use BEAST2.

https://www.beast2.org/2020/12/15/ORC.html

To view this discussion on the web visit https://groups.google.com/d/msgid/beast-users/CAABJSX0TnKt%3DvRkxQ2R_xVAZ7v%3DZ_B5JUFAYgOpGTYyQkjTjoQ%40mail.gmail.com.

Enviado via UCSMail.