beast-users

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Alexandra Gavryushkina, … Artem B4

Nov 20

BEAST2 gives errors when using BEAGLE

Hi Sasha, Unchecking this box disables BEAGLE. It's strange since the problem usually arises with

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BEAST2 gives errors when using BEAGLE

Hi Sasha, Unchecking this box disables BEAGLE. It's strange since the problem usually arises with

Nov 20

Klara Asselin, Tim Vaughan2

Nov 20

ReMASTER tree generation fail

Hi Klara, What kind of trajectory simulation approach are you using? Deterministic (ie ODE

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ReMASTER tree generation fail

Hi Klara, What kind of trajectory simulation approach are you using? Deterministic (ie ODE

Nov 20

Martin Gunnill, … Remco Bouckaert3

Nov 19

WSL conda BEAST 2.6.3 'A fatal error has been detected by the Java Runtime Environment:.....''

Hi Esben Not sure how Conda, WSL, BEAST and BEAGLE interact, but have you considered using the latest

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WSL conda BEAST 2.6.3 'A fatal error has been detected by the Java Runtime Environment:.....''

Hi Esben Not sure how Conda, WSL, BEAST and BEAGLE interact, but have you considered using the latest

Nov 19

Alexei Drummond, Artem B2

Nov 18

BEAST 2 user and developer experience and future development survey

Hi Alexei, I forgot to mention some points in the survey. - As far as I remember, BEAST 1.X is not

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BEAST 2 user and developer experience and future development survey

Hi Alexei, I forgot to mention some points in the survey. - As far as I remember, BEAST 1.X is not

Nov 18

Jaiane Oliveira, … Artem B5

Nov 18

Divergence time

Hey Jaiane, Unfortunately, I'm not a great specialist in internal node dating, but I'll try

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Divergence time

Hey Jaiane, Unfortunately, I'm not a great specialist in internal node dating, but I'll try

Nov 18

JULEN AIZPURUA IRAOLA, Pfeiffer, Wayne3

Nov 18

Beast 1.10.4 Running forever

Hi Wayne, Thank you so much for your response. I'll try reducing the partition and running it on

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Beast 1.10.4 Running forever

Hi Wayne, Thank you so much for your response. I'll try reducing the partition and running it on

Nov 18

Nov 17

SNAPP convergence issue

Hi, Thank your for the support in this group and with the documentation. Despite looking at the

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SNAPP convergence issue

Hi, Thank your for the support in this group and with the documentation. Despite looking at the

Nov 17

Nov 17

Clade constraints, FBD

Hi all, My apologies if this is a repeated post, I thought I had already inquired about this but can

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Clade constraints, FBD

Hi all, My apologies if this is a repeated post, I thought I had already inquired about this but can

Nov 17

Nov 17

FBD: fixed tree, variably constrained fossils

Hi all, I am hoping to set up an FBD inference but have run into a couple of questions. This would be

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FBD: fixed tree, variably constrained fossils

Hi all, I am hoping to set up an FBD inference but have run into a couple of questions. This would be

Nov 17

Nov 17

"java.lang.ArrayIndexOutOfBoundsException" errors while running SNAPP

Hi， I am using Beast v2.7.7 to estimates divergence time on linux with SNP data, but I encountered

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"java.lang.ArrayIndexOutOfBoundsException" errors while running SNAPP

Hi， I am using Beast v2.7.7 to estimates divergence time on linux with SNP data, but I encountered

Nov 17

lilne...@gmail.com, … Ales Bucek3

Nov 17

Running fine, but suddenly met with org.apache.commons.math.MathRuntimeException$4: standard deviation must be positive (0)

Same here, after 83757000 samples. Did you find any explanation for the error? On Friday, July 5,

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Running fine, but suddenly met with org.apache.commons.math.MathRuntimeException$4: standard deviation must be positive (0)

Same here, after 83757000 samples. Did you find any explanation for the error? On Friday, July 5,

Nov 17

Nov 17

Error when opening XML file

Hello I receive this error when attempting to re-run the linked file in BEAST v.10.5.0. "Error

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Error when opening XML file

Hello I receive this error when attempting to re-run the linked file in BEAST v.10.5.0. "Error

Nov 17

Nov 14

Genomic/transcriptomic dataset and BEAST

Hello, I have a mammal dataset of ~40 taxa, but with about 10000 genes it's too long really for

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Genomic/transcriptomic dataset and BEAST

Hello, I have a mammal dataset of ~40 taxa, but with about 10000 genes it's too long really for

Nov 14

Nov 12

Error at the beginning of stepping stone sampling when using UCLN/Skygrid or Strict/Skygrid combinations

Hello, Our runs are failing when using the UCLN or Strict clock models combined with the Skygrid

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Error at the beginning of stepping stone sampling when using UCLN/Skygrid or Strict/Skygrid combinations

Hello, Our runs are failing when using the UCLN or Strict clock models combined with the Skygrid

Nov 12

Oct 30

I would like to renew my question. kind regards, M Mathias L schrieb am Donnerstag, 23. November 2023

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I would like to renew my question. kind regards, M Mathias L schrieb am Donnerstag, 23. November 2023

Oct 30

Vaca, … Morgan Geniviva4

Oct 30

collection data

Dear Omar, please can you help me in which way I can prepare dataset for phylogeographic analysis in

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collection data

Dear Omar, please can you help me in which way I can prepare dataset for phylogeographic analysis in

Oct 30

Morgan Geniviva

Oct 29

oscillating age(root) trace for partitioned HIV-1 pol sequences

Hi everyone, I am running an analysis of HIV-1 pol sequences using 3 partitions (recombinant

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oscillating age(root) trace for partitioned HIV-1 pol sequences

Hi everyone, I am running an analysis of HIV-1 pol sequences using 3 partitions (recombinant

Oct 29

Gabriel Diorio Batista, … Dylan O'Hearn4

Oct 29

Challenges in Using BEAST for Intraspecific Phylogenetic Analysis and Divergence Time Estimation

Regarding the tree prior, a birth-death tree prior has been shown to be superior to the yule for

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Challenges in Using BEAST for Intraspecific Phylogenetic Analysis and Divergence Time Estimation

Regarding the tree prior, a birth-death tree prior has been shown to be superior to the yule for

Oct 29

Alfredo Bruno, Alexei Drummond6

Oct 24

Question about Evolutionary history of the complete genome of respiratory syncytial virus type A and B

As long as you have specified the tip dates of your sequences then the "clock rate" will be

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Question about Evolutionary history of the complete genome of respiratory syncytial virus type A and B

As long as you have specified the tip dates of your sequences then the "clock rate" will be

Oct 24

Conor O'Hare, … JT McCrone6

Oct 24

Thorney Likelihood - Template File

Hello, Sorry I missed these initial messages. There are some xml compatibility issues in using

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Thorney Likelihood - Template File

Hello, Sorry I missed these initial messages. There are some xml compatibility issues in using

Oct 24

Oct 22

Babel use on an MCC tree from MASCOT

Hi there, been using Babel in BEAST 2.7 to work out raw transition counts between states on a trees

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Babel use on an MCC tree from MASCOT

Hi there, been using Babel in BEAST 2.7 to work out raw transition counts between states on a trees

Oct 22

Verena Ashford, Omar Mejía2

Oct 22

Questions about tip-dating and Bayesian skyline plots

Hi Verena, When you refer to ancient DNA I guess you are dealing with archaeological or similar

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Questions about tip-dating and Bayesian skyline plots

Hi Verena, When you refer to ancient DNA I guess you are dealing with archaeological or similar

Oct 22

William Fernando Chaparro-Pico, … Alfredo Bruno3

Oct 22

Information for a beginner

Dear colleagues. I am trying to build the evolutionary history of the complete genome of respiratory

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Information for a beginner

Dear colleagues. I am trying to build the evolutionary history of the complete genome of respiratory

Oct 22

Oct 15

pathsampling does not start if Shrinkage local clock is implemented

I ran a beast analysis implementing Shrinkage local clock model in BEAST Version v10.5.0-beta4

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pathsampling does not start if Shrinkage local clock is implemented

I ran a beast analysis implementing Shrinkage local clock model in BEAST Version v10.5.0-beta4

Oct 15

Oct 14

Using ClaDS for evolutionary rate estimation

Hi all, I am trying to use ClaDS within BEAST2 to do branch rate estimation for a time calibrated

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Using ClaDS for evolutionary rate estimation

Hi all, I am trying to use ClaDS within BEAST2 to do branch rate estimation for a time calibrated

Oct 14

Samuel Lam, Bushra Shahid3

Oct 13

Error while running SNAPP

Hi Bushra, I don't remember it clearly, but there must be problems with the .xml files generated

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Error while running SNAPP

Hi Bushra, I don't remember it clearly, but there must be problems with the .xml files generated

Oct 13

Oct 12

Thorney BEAST with MarkovJumpsTreeLikelihood OpenCL issue

Hi Everyone, currently i trying to do some phlyogeography analysis and right now I want to confirm if

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Thorney BEAST with MarkovJumpsTreeLikelihood OpenCL issue

Hi Everyone, currently i trying to do some phlyogeography analysis and right now I want to confirm if

Oct 12

Zoe Holzer, higg...@gmail.com5

Oct 9

Getting interval endpoints / time population size pairs from BICEPS output

It does, thanks so much! On Tuesday, October 8, 2024 at 6:14:56 PM UTC-7 higg...@gmail.com wrote: Hi

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Getting interval endpoints / time population size pairs from BICEPS output

It does, thanks so much! On Tuesday, October 8, 2024 at 6:14:56 PM UTC-7 higg...@gmail.com wrote: Hi

Oct 9

Oct 8

TreeSelector.jar

Hello Fellow BEAST Users, "I'm trying to perform a discrete trait analysis in BEAST v1.10.4

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TreeSelector.jar

Hello Fellow BEAST Users, "I'm trying to perform a discrete trait analysis in BEAST v1.10.4

Oct 8

Alejandro Piña Iturbe, Artem B3

Oct 8

Running Generalized stepping-stone by separate

Thank you Artem for your help. Alejandro El lun, 7 oct 2024 a las 22:56, Artem B (<ui.artem.ui@

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Running Generalized stepping-stone by separate

Thank you Artem for your help. Alejandro El lun, 7 oct 2024 a las 22:56, Artem B (<ui.artem.ui@

Oct 8

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