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Welcome to revbayes-users, a forum and mailing list to discuss RevBayes-related topics, including: RevBayes installation and use, scripting and programming, phylogenetics, population genetics, models of evolution, graphical models, etc.

If you wish to report a bug in RevBayes, use our GitHub Issues page.

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3/29/17

Guidelines to request help with RevBayes

This post is meant for researchers who'd like help using RevBayes, such as help specifying new

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Guidelines to request help with RevBayes

This post is meant for researchers who'd like help using RevBayes, such as help specifying new

3/29/17

Sophie Newmarch2

Aug 17

Revbayes terminal not executing script from RevStudio on Windows

Just to update here as well. It turned out that I had a typo when reading in some stratified matrices

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Revbayes terminal not executing script from RevStudio on Windows

Just to update here as well. It turned out that I had a typo when reading in some stratified matrices

Aug 17

Sophie Newmarch2

Aug 17

Time-stratified distance matrices

Hi all, Just an update on this topic in case someone else (likely beginners like me!) would find it

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Time-stratified distance matrices

Hi all, Just an update on this topic in case someone else (likely beginners like me!) would find it

Aug 17

Jul 2

Plugin not registered?

I installed tensorphylo and revbayes following the README instructions and they both said they were

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Plugin not registered?

I installed tensorphylo and revbayes following the README instructions and they both said they were

Jul 2

Jul 1

Issue installing RevBayes for TensorPhylo

Hi all, I am trying to install RevBayes for TensorPhylo following the README instructions. I get all

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Issue installing RevBayes for TensorPhylo

Hi all, I am trying to install RevBayes for TensorPhylo following the README instructions. I get all

Jul 1

Jun 16

RevGadgets - choose node states in ASE tree

Hi all, With the caveat that RevGadgets is its own animal, I wonder if anyone has some tips here. I

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RevGadgets - choose node states in ASE tree

Hi all, With the caveat that RevGadgets is its own animal, I wonder if anyone has some tips here. I

Jun 16

MUHAMMAD REHAN, Benjamin Redelings2

May 30

How does RevBayes treat missing character states?

Hi Rehan, 1. Missing character states are treated as a lack of knowledge of the what the state is --

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How does RevBayes treat missing character states?

Hi Rehan, 1. Missing character states are treated as a lack of knowledge of the what the state is --

May 30

Daniel Vasquez Restrepo, Ziv Lieberman2

May 26

Dating with a fixed tree

Hi Daniel, I may be misunderstanding some combination of your goal and what the tutorial does, but on

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Dating with a fixed tree

Hi Daniel, I may be misunderstanding some combination of your goal and what the tutorial does, but on

May 26

Ivan Magalhães

May 21

Using "known" substitution rates to calibrate the clock

Hello everyone, I am new to RevBayes I have been able to calibrate a time tree by setting ages to

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Using "known" substitution rates to calibrate the clock

Hello everyone, I am new to RevBayes I have been able to calibrate a time tree by setting ages to

May 21

Yang ZHAO, Benjamin Redelings3

May 5

cannot be located in the dynamic link library

yeah, it works after redownload, thanks. On Monday, 5 May 2025 at 15:32:41 UTC+2 benjamin....@gmail.

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cannot be located in the dynamic link library

yeah, it works after redownload, thanks. On Monday, 5 May 2025 at 15:32:41 UTC+2 benjamin....@gmail.

May 5

Mar 26

Announcement: RevBayes Office Hours April 2 at 7:00 PM Central US Time

Dear RevBayes Community: Several members of the RevBayes Developer Team are hosting virtual office

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Announcement: RevBayes Office Hours April 2 at 7:00 PM Central US Time

Dear RevBayes Community: Several members of the RevBayes Developer Team are hosting virtual office

Mar 26

Hee Han, Benjamin Redelings2

Mar 8

Data file not found Error

Hi Hee Han, Revbayes says that the file is not found. Have you checked that the file is in the right

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Data file not found Error

Hi Hee Han, Revbayes says that the file is not found. Have you checked that the file is in the right

Mar 8

Manel Aitelhadj, Benjamin Redelings3

11/19/24

BM tutorial : could not compute lnProb for node

Can you repost this here? https://github.com/revbayes/revbayes/discussions -BenRI On 11/18/24 6:56 AM

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BM tutorial : could not compute lnProb for node

Can you repost this here? https://github.com/revbayes/revbayes/discussions -BenRI On 11/18/24 6:56 AM

11/19/24

Benjamin Redelings

11/15/24

New discussion forum

Hi everyone, We have opened a new discussion forum for revbayes here: https://github.com/revbayes/

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New discussion forum

Hi everyone, We have opened a new discussion forum for revbayes here: https://github.com/revbayes/

11/15/24

Torsten Hauffe2

11/7/24

Cannot drop tip from proposed phylogeny

I solved the problem of dropping tip from a sampled phylogeny by using the fnPruneTree() function. On

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Cannot drop tip from proposed phylogeny

I solved the problem of dropping tip from a sampled phylogeny by using the fnPruneTree() function. On

11/7/24

Ziv Lieberman, … Benjamin Redelings7

11/6/24

Soft topological constraints

I'm thinking about adding pseudodata for tree constraints, so that instead of making the

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Soft topological constraints

I'm thinking about adding pseudodata for tree constraints, so that instead of making the

11/6/24

10/31/24

Convenience R Package NaN argument error

Hi all, I am new to using the convenience R package, and I need some help loading in my tree file to

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Convenience R Package NaN argument error

Hi all, I am new to using the convenience R package, and I need some help loading in my tree file to

10/31/24

Sophie Seidel, Benjamin Redelings3

10/10/24

Error when loading PoMo data

For anyone having the same issue: The response to my issue on github (https://github.com/revbayes/

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Error when loading PoMo data

For anyone having the same issue: The response to my issue on github (https://github.com/revbayes/

10/10/24

Nathanael Walker-Hale2

9/19/24

Advice on tree prior for constrained analysis of within and between species sampling

wary*! An ironic typo... On Thursday, September 19, 2024 at 1:22:41 PM UTC+1 Nathanael Walker-Hale

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Advice on tree prior for constrained analysis of within and between species sampling

wary*! An ironic typo... On Thursday, September 19, 2024 at 1:22:41 PM UTC+1 Nathanael Walker-Hale

9/19/24

Zachary Griebenow, David Černý2

8/21/24

Backbone topology, non-FBD

Hi Zach, It's not true that dnConstrainedTopology requires FBD as the base distribution; it's

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Backbone topology, non-FBD

Hi Zach, It's not true that dnConstrainedTopology requires FBD as the base distribution; it's

8/21/24

7/16/24

Best transition model for microsatellites?

I would like to model microsatellites. These are genomic elements with 2, 3, or 4 bp repeating motifs

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Best transition model for microsatellites?

I would like to model microsatellites. These are genomic elements with 2, 3, or 4 bp repeating motifs

7/16/24

Caroline Siegert, Benjamin Redelings5

7/15/24

FBD changes with updates?

Oh, and I should say that from what I heard, the earlier version of revbayes probably also has a bug

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FBD changes with updates?

Oh, and I should say that from what I heard, the earlier version of revbayes probably also has a bug

7/15/24

Martin R. Smith

7/8/24

Subtracting log-likelihoods within a model

I'm implementing a model in RevBayes. Tersely, I observe data x under the model M(θ) with

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Subtracting log-likelihoods within a model

I'm implementing a model in RevBayes. Tersely, I observe data x under the model M(θ) with

7/8/24

Jan Bührer, Hong-Wun Chen (Hong-Wun Chen)4

5/20/24

Error when applying characterMapTree() function

It works for me when you define a filename to store the shift_prob_file. Somehow the default = NULL

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Error when applying characterMapTree() function

It works for me when you define a filename to store the shift_prob_file. Somehow the default = NULL

5/20/24

Igor Yanovich, Torsten Hauffe2

5/17/24

traversing the branches in Rev - which branches are adjacent?

Hi Igor, The tutorial on relaxed Brownian motion shows how to specify an autocorrelated clock by

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traversing the branches in Rev - which branches are adjacent?

Hi Igor, The tutorial on relaxed Brownian motion shows how to specify an autocorrelated clock by

5/17/24

5/15/24

Issue with taxon object for dnMultiSpeciesCoalescentUniformPrior RB 1.2.3

Hi, Does anyone knows how the taxon object for dnMultiSpeciesCoalescentUniformPrior needs to look

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Issue with taxon object for dnMultiSpeciesCoalescentUniformPrior RB 1.2.3

Hi, Does anyone knows how the taxon object for dnMultiSpeciesCoalescentUniformPrior needs to look

5/15/24

Peter Wagner, Orlando Schwery2

5/10/24

fbd_tree ~ dnConstrainedTopology(fbd_dist,constraints=constraints) gets hungup.

I think one of the bug fixes in v1.2.3 fixed that for a case using dnConstrainedTopology on

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fbd_tree ~ dnConstrainedTopology(fbd_dist,constraints=constraints) gets hungup.

I think one of the bug fixes in v1.2.3 fixed that for a case using dnConstrainedTopology on

5/10/24

Zachary Griebenow

5/7/24

Starting probability for given parameter not computable

Greetings all, I'm encountering an issue that has been noted on this forum, but for which I

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Starting probability for given parameter not computable

Greetings all, I'm encountering an issue that has been noted on this forum, but for which I

5/7/24

Manel Aitelhadj

4/4/24

Brownian motion tutorial script

Hi, I am currently doing the BM tutorial on RevBayes (https://revbayes.github.io/tutorials/

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Brownian motion tutorial script

Hi, I am currently doing the BM tutorial on RevBayes (https://revbayes.github.io/tutorials/

4/4/24

Zachary Griebenow

3/26/24

Node-dating with fully constrained topology

Greetings all, I am attempting node-dating with a fully constrained, bifurcating a priori topology.

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Node-dating with fully constrained topology

Greetings all, I am attempting node-dating with a fully constrained, bifurcating a priori topology.

3/26/24

3/21/24

problem with RevGadgets

Hi there, I am using RevGadgets for visualization of the result of a lineage-specific diversification

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problem with RevGadgets

Hi there, I am using RevGadgets for visualization of the result of a lineage-specific diversification

3/21/24

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