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12:36 PM

bModel Test's strange performance under different operating systems

Hello everyone. I meet a knotty problem when I perform bModelTest under BEAST2. The identical data

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bModel Test's strange performance under different operating systems

Hello everyone. I meet a knotty problem when I perform bModelTest under BEAST2. The identical data

12:36 PM

Michael Charleston, Marc Suchard3

Jan 23

Thanks Marc, I've come to the same conclusions: while I haven't got to the bottom of why it

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Thanks Marc, I've come to the same conclusions: while I haven't got to the bottom of why it

Jan 23

Corné van der Linden, Remco Bouckaert3

Jan 20

Downloading OBAMA on a Linux server

Hi Remco, Thank you for moving OBAMA. I have tried your suggestion: ~/Programs/beast/bin/

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Downloading OBAMA on a Linux server

Hi Remco, Thank you for moving OBAMA. I have tried your suggestion: ~/Programs/beast/bin/

Jan 20

Umanga Gunasekera, Caine Barlow2

Jan 20

SPREAD3 not accepting the txt file

Hi All, I am having the same problem. Anyone have a solution. Cheers, Caine. On Wednesday, February

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SPREAD3 not accepting the txt file

Hi All, I am having the same problem. Anyone have a solution. Cheers, Caine. On Wednesday, February

Jan 20

Cristopher Reyes

Jan 20

Error running BEAST v2.6.6

Hello everyone, I am using BEAST for the first time and still figuring out how to make it work. I had

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Error running BEAST v2.6.6

Hello everyone, I am using BEAST for the first time and still figuring out how to make it work. I had

Jan 20

Jan 19

MC3 option in BEAST v1.10.4

Hello, I try to run MC3 in BEAST v1.10.4, but it stops without giving any error message. I try to run

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MC3 option in BEAST v1.10.4

Hello, I try to run MC3 in BEAST v1.10.4, but it stops without giving any error message. I try to run

Jan 19

Chris Ruis, … maryam almasi4

Jan 18

BEAST2 substitution tree

Hi, I am using Beast v.1.10.4. There is a box with this title 'create tree log file with branch

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BEAST2 substitution tree

Hi, I am using Beast v.1.10.4. There is a box with this title 'create tree log file with branch

Jan 18

Jan 13

identifying well-supported rates

Dear all, Please can you help me how to identify well-supported rates between locations in continuous

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identifying well-supported rates

Dear all, Please can you help me how to identify well-supported rates between locations in continuous

Jan 13

Jan 13

Repeating BEAST 1.8.4 returns a parsing error

hello, Having made some changes in the nexus file only, I tried to repeat the run of an old xml file.

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Repeating BEAST 1.8.4 returns a parsing error

hello, Having made some changes in the nexus file only, I tried to repeat the run of an old xml file.

Jan 13

Jan 12

Error 110 parsing the xml input file

Hello, I'm trying to run beast in supercomputers that can't connect to the Internet, and

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Error 110 parsing the xml input file

Hello, I'm trying to run beast in supercomputers that can't connect to the Internet, and

Jan 12

ithi...@hotmail.com, idrissa dieng2

Jan 12

ParticleFilter AND coupledMCMC

Hi all i run discrete phylogeographic analysis but i have low BF for location transition ; i need

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ParticleFilter AND coupledMCMC

Hi all i run discrete phylogeographic analysis but i have low BF for location transition ; i need

Jan 12

Paolo Caputo, Remco Bouckaert2

Jan 11

StarBeast2 convergence problems (possibly not depending on generations)

Hi Paolo, You mentioned observing positive likelihoods. Priors can become positive, since they are

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StarBeast2 convergence problems (possibly not depending on generations)

Hi Paolo, You mentioned observing positive likelihoods. Priors can become positive, since they are

Jan 11

Ana Bedoya, … Remco Bouckaert4

Jan 10

Calibrated Yule model with low ESS after 1 billion generations

HI Ana, Since the birth rate and ucldMean parameters have low ESS, perhaps increasing the operator

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Calibrated Yule model with low ESS after 1 billion generations

HI Ana, Since the birth rate and ucldMean parameters have low ESS, perhaps increasing the operator

Jan 10

Jan 9

Would you tell me how to use Hamiltonian Monte Carlo sampling method in Beast?

Hello, I tried to use the Hamiltonian Monte Carlo sampling method (HMC) in Beast. Because I cannot

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Would you tell me how to use Hamiltonian Monte Carlo sampling method in Beast?

Hello, I tried to use the Hamiltonian Monte Carlo sampling method (HMC) in Beast. Because I cannot

Jan 9

geo, … nicolad...@gmail.com7

Jan 7

Hi Danny, I am afraid that the BASTA template will not work with BEAUti, but it would require editing

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Hi Danny, I am afraid that the BASTA template will not work with BEAUti, but it would require editing

Jan 7

Jan 2

Is it possible to open 500m matrix with StarBeast?

Hello, everyone, I am trying to input a matrix (500m, 160 individuals, 60 species) into BEAUTi with

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Is it possible to open 500m matrix with StarBeast?

Hello, everyone, I am trying to input a matrix (500m, 160 individuals, 60 species) into BEAUTi with

Jan 2

Samuel Zimmerman

Jan 2

setting priors for Path Sampling/Stepping-stone sampling

Hi all, I recently ran Beast to perform divergence dating on a species of bacteria using several

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setting priors for Path Sampling/Stepping-stone sampling

Hi all, I recently ran Beast to perform divergence dating on a species of bacteria using several

Jan 2

J, Sam Zimmerman3

Jan 2

Markov chain parameters for BSP

Hi J. Sorry for the overdue response, but I am also very curious about the Markov Chain parameters

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Markov chain parameters for BSP

Hi J. Sorry for the overdue response, but I am also very curious about the Markov Chain parameters

Jan 2

Jan 2

Enquiry on <twoEpoch> function

Dear all, I am running 2-epoch model to estimate mutation rate following expansion dating method of

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Enquiry on <twoEpoch> function

Dear all, I am running 2-epoch model to estimate mutation rate following expansion dating method of

Jan 2

Jane, … Ales Bucek8

Jan 2

Errors finding likelihood.log and beast.xml.state files

I noticed that the error with missing *.xml.state file occurs also when attempting to resume a BEAST

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Errors finding likelihood.log and beast.xml.state files

I noticed that the error with missing *.xml.state file occurs also when attempting to resume a BEAST

Jan 2

Sakshi Kamboj, Brandon Stark2

12/20/21

Difficulty in interpreting TempEST output

no temporal signal for your data. 在2021年12月1日星期三 UTC+8 01:00:47<Sakshi Kamboj> 写道： Hi all I am

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Difficulty in interpreting TempEST output

no temporal signal for your data. 在2021年12月1日星期三 UTC+8 01:00:47<Sakshi Kamboj> 写道： Hi all I am

12/20/21

12/19/21

The individual components of the posterior are as follows: The initial posterior is zero:

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The individual components of the posterior are as follows: The initial posterior is zero:

12/19/21

Wolfgang Wüster, Brandon Stark2

12/19/21

BEAST 1.10.4 suddenly can't find BEAGLE resources on MAC

which version of your bealge? 在2021年12月7日星期二 UTC+8 01:10:02<wolfgan...@gmail.com> 写道： Hello

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BEAST 1.10.4 suddenly can't find BEAGLE resources on MAC

which version of your bealge? 在2021年12月7日星期二 UTC+8 01:10:02<wolfgan...@gmail.com> 写道： Hello

12/19/21

12/6/21

Prior log-probability is -Inf with MRCA offset age

Hi all, I fail to start a Beast2 run (v2.6.6) when specifying an "offset" in the MRCA prior

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Prior log-probability is -Inf with MRCA offset age

Hi all, I fail to start a Beast2 run (v2.6.6) when specifying an "offset" in the MRCA prior

12/6/21

12/6/21

Infinite log probability when MRCA prior for age is offset

Hi all, I fail to run Beast (v2.6.6) for molecular dating with 20 sequences of Primates. In short,

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Infinite log probability when MRCA prior for age is offset

Hi all, I fail to run Beast (v2.6.6) for molecular dating with 20 sequences of Primates. In short,

12/6/21

Garima, Remco Bouckaert2

12/2/21

BEAST - JAVA error or not?

Indeed, it looks like java ran out of memory. To increase available memory, see here: http://www.

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BEAST - JAVA error or not?

Indeed, it looks like java ran out of memory. To increase available memory, see here: http://www.

12/2/21

Eduardo Ascarrunz

12/2/21

Starbeast3 species. tree model missing in BEAUti

Hi everyone, I am following the tutorial for Starbeast3 in BEAUti with the Starbeast3 template, but I

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Starbeast3 species. tree model missing in BEAUti

Hi everyone, I am following the tutorial for Starbeast3 in BEAUti with the Starbeast3 template, but I

12/2/21

12/1/21

divergence time estimation with known mutation rates

Hello all, This is a minor question, but I want to make sure I am setting up a divergence estimation

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divergence time estimation with known mutation rates

Hello all, This is a minor question, but I want to make sure I am setting up a divergence estimation

12/1/21

11/30/21

Lognormal parameters

I am trying to specify the lognormal in Beast2 for the relaxed clock. Usually the lognormal

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Lognormal parameters

I am trying to specify the lognormal in Beast2 for the relaxed clock. Usually the lognormal

11/30/21

11/30/21

GLM linking covariates to logNe, following Gill (2016) and Dellicour (2020)

Hi, I wrote a python script add covariates to XML generated from BEAUti (see below). Ran this on a

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GLM linking covariates to logNe, following Gill (2016) and Dellicour (2020)

Hi, I wrote a python script add covariates to XML generated from BEAUti (see below). Ran this on a

11/30/21

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