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Bist, Bhuwan Singh
,
Antonio Gomez
2
Jul 25
Calibration error
Hi Bhuwan, I suspect it has a lot to do with your priors (of course), particularly your MRCA prior
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Calibration error
Hi Bhuwan, I suspect it has a lot to do with your priors (of course), particularly your MRCA prior
Jul 25
Bist, Bhuwan Singh
Jul 24
Error 130 parsing the xml input file
Hi all, The second codon position has a substitution as TVM+F+I+G4 but the option for TVM is not in
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Error 130 parsing the xml input file
Hi all, The second codon position has a substitution as TVM+F+I+G4 but the option for TVM is not in
Jul 24
MKPUMA NICODEMUS
,
Alexei Drummond
2
Jul 22
Inability to generate MCC tree
Is it possible you might be setting your burnin incorrectly? It says ignoring the first 30000000
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Inability to generate MCC tree
Is it possible you might be setting your burnin incorrectly? It says ignoring the first 30000000
Jul 22
Aline Méndez-Rodríguez
2
Jul 22
Fixed Tree Analysis
xml https://drive.google.com/file/d/1wvFOFcRWVWJPs59jPLG9WV2oPoBNca2V/view?usp=sharing El domingo, 21
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Fixed Tree Analysis
xml https://drive.google.com/file/d/1wvFOFcRWVWJPs59jPLG9WV2oPoBNca2V/view?usp=sharing El domingo, 21
Jul 22
Jaiane Oliveira
,
Alexei Drummond
3
Jul 21
BEAUTI
Hello. This is the error that appears when trying to load the NEXUS file. Em sex., 19 de jul. de 2024
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BEAUTI
Hello. This is the error that appears when trying to load the NEXUS file. Em sex., 19 de jul. de 2024
Jul 21
Brian Dorsey
2
Jul 19
Likelihood/posterior very different between machines - even resuming run
I forgot to mention that, on the Mac Studio only, there is a sum reported between mcmc steps (see
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Likelihood/posterior very different between machines - even resuming run
I forgot to mention that, on the Mac Studio only, there is a sum reported between mcmc steps (see
Jul 19
Priscila Souza
,
Omar Mejía
2
Jul 19
Error Reading file: Beauti
Priscila, The error suggest that some information is missing, it would be easy if you attach your
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Error Reading file: Beauti
Priscila, The error suggest that some information is missing, it would be easy if you attach your
Jul 19
Antonio Gomez
,
higg...@gmail.com
4
Jul 14
Fixed Tree Analysis Fixed topology estimate branch lengths error
Yes, that makes sense -- otherwise the clock rate will just sample from the prior, which is probably
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Fixed Tree Analysis Fixed topology estimate branch lengths error
Yes, that makes sense -- otherwise the clock rate will just sample from the prior, which is probably
Jul 14
Brian Dorsey
Jul 11
Path Sampling divide by zero error - workaround
Hi all, Beast 2.7.7 snapper 1.1.4 Mac Studio M1 Ultra I'm trying to set up a snapper path
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Path Sampling divide by zero error - workaround
Hi all, Beast 2.7.7 snapper 1.1.4 Mac Studio M1 Ultra I'm trying to set up a snapper path
Jul 11
Jaiane Oliveira
,
Gaspary Eugene
5
Jul 9
XML BEAUTI
Dear Jaiane, csv file should contain two columns column accession no/taxa id and dates preferable in
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XML BEAUTI
Dear Jaiane, csv file should contain two columns column accession no/taxa id and dates preferable in
Jul 9
Tiago Simoes
, …
Omar Mejía
6
Jul 9
FixedTreeAnalysis error for Import Tree
Dear Dylan: I have attached the instructions on how to deal with forcing a tree topology in Beast:
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FixedTreeAnalysis error for Import Tree
Dear Dylan: I have attached the instructions on how to deal with forcing a tree topology in Beast:
Jul 9
Wonseop Lim
,
Kylie
3
Jul 8
Availability of FLC packages on BEAST 2.7
Hi Kylie, Thank you! I now have full set of clock models for my analysis.
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Availability of FLC packages on BEAST 2.7
Hi Kylie, Thank you! I now have full set of clock models for my analysis.
Jul 8
Wonseop Lim
, …
Artem B
8
Jul 8
Linearly increasing prior trace plot when using random local clock model
1. Thank you Artem! However, I tried all the options I could think of (as long as they lead to
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Linearly increasing prior trace plot when using random local clock model
1. Thank you Artem! However, I tried all the options I could think of (as long as they lead to
Jul 8
Zade Alafranji
,
Gaspary Eugene
2
Jul 8
trouble reaching convergence with BEAST2
Hi Zade, To my opinion I normally start with baseline model coalescent constant pollution just to see
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trouble reaching convergence with BEAST2
Hi Zade, To my opinion I normally start with baseline model coalescent constant pollution just to see
Jul 8
lilne...@gmail.com
,
Utpal Smart
2
Jul 5
Running fine, but suddenly met with org.apache.commons.math.MathRuntimeException$4: standard deviation must be positive (0)
Hi, I am running into the exact same issue. Were you able to figure it out? Thanks, On Friday,
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Running fine, but suddenly met with org.apache.commons.math.MathRuntimeException$4: standard deviation must be positive (0)
Hi, I am running into the exact same issue. Were you able to figure it out? Thanks, On Friday,
Jul 5
章瑶瑶
Jul 4
BFD SNAPP HELP
Hi everyone, When I using SNAPP to evaluate the BFD factor model, I encountered an error. I followed
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BFD SNAPP HELP
Hi everyone, When I using SNAPP to evaluate the BFD factor model, I encountered an error. I followed
Jul 4
CJ Battey
, …
章瑶瑶
21
Jul 4
error with BEAST2.2.0 SNAPP+MODEL_SELECTION
Have you solved the problem? I met the same error. 在2024年6月29日星期六 UTC+8 02:32:41<Elizabeth Collins
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error with BEAST2.2.0 SNAPP+MODEL_SELECTION
Have you solved the problem? I met the same error. 在2024年6月29日星期六 UTC+8 02:32:41<Elizabeth Collins
Jul 4
Dylan O'Hearn
Jul 1
ORC Priors
Hello, I'm performing a concatenated analysis of mtDNA and nuclear data and I'm partitioning
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ORC Priors
Hello, I'm performing a concatenated analysis of mtDNA and nuclear data and I'm partitioning
Jul 1
Haley Arnold
,
michaelm
2
Jun 30
Inferring divergence time from SNP data in SNAPP?
Dear Haley, Perhaps this tutorial might be useful: https://github.com/ForBioPhylogenomics/tutorials/
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Inferring divergence time from SNP data in SNAPP?
Dear Haley, Perhaps this tutorial might be useful: https://github.com/ForBioPhylogenomics/tutorials/
Jun 30
lncespe...@gmail.com
,
Monica Ó Fathaigh
3
Jun 29
very low ESS in SNAPPER runs (help!)
Hi Monica, Thank you so much for your thorough answer! I am already trying to figure out what is the
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very low ESS in SNAPPER runs (help!)
Hi Monica, Thank you so much for your thorough answer! I am already trying to figure out what is the
Jun 29
Chucho Diaz-Cruz
,
higg...@gmail.com
3
Jun 27
drag and drop & run error
Indeed, that was the problem with my dataset. Thank you so much. El jueves, 27 de junio de 2024 a las
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drag and drop & run error
Indeed, that was the problem with my dataset. Thank you so much. El jueves, 27 de junio de 2024 a las
Jun 27
magnus...@gmail.com
, …
Wonseop Lim
7
Jun 25
Ok to combine bmodeltest with nested sampling?
Hi Magnus, I know that this feed has not been active for a long time, but I am having some trouble
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Ok to combine bmodeltest with nested sampling?
Hi Magnus, I know that this feed has not been active for a long time, but I am having some trouble
Jun 25
BLANCA MARÍA ROJAS ANDRÉS
2
Jun 25
Error with operator for birthDeath.sampleProbability
Hi again, I forgot to mention that I am using BEAST v1.10.4. Here is the xml file, just in case is
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Error with operator for birthDeath.sampleProbability
Hi again, I forgot to mention that I am using BEAST v1.10.4. Here is the xml file, just in case is
Jun 25
Monica Ó Fathaigh
, …
Remco Bouckaert
7
Jun 24
Error - Coupled MCMC with Speedemon?
Thanks Monica, DensiTree should not be a seperate BEAST 2 package, it is just part of the
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Error - Coupled MCMC with Speedemon?
Thanks Monica, DensiTree should not be a seperate BEAST 2 package, it is just part of the
Jun 24
Remco Bouckaert
Jun 24
BEAST v2.7.7 released
Dear BEAST user, We are pleased to announce the release of BEAST v2.7.7. The main changes are: o Add
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BEAST v2.7.7 released
Dear BEAST user, We are pleased to announce the release of BEAST v2.7.7. The main changes are: o Add
Jun 24
Yanina Briñoccoli
,
Gaspary Eugene
4
Jun 21
java.lang.RuntimeException: Cannot find taxon 1-78 in data
Thank you very much! The mistake was that there is no sequence "1-78" as such, but that the
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java.lang.RuntimeException: Cannot find taxon 1-78 in data
Thank you very much! The mistake was that there is no sequence "1-78" as such, but that the
Jun 21
Jaiane Oliveira
, …
higg...@gmail.com
4
Jun 20
Treeannotator
With BEAST v2.7, java is included with the distribution, so TreeAnnotator should always have the
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Treeannotator
With BEAST v2.7, java is included with the distribution, so TreeAnnotator should always have the
Jun 20
Fabricia
Jun 20
Spread3 command line
Hello, I am trying to sumarize the Bayes Factor using SPREAD3 using the command line but I get an
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Spread3 command line
Hello, I am trying to sumarize the Bayes Factor using SPREAD3 using the command line but I get an
Jun 20
peterpan10
Jun 19
relaxed clock with thorney likelihood
Hello BEASTies, Anyone know how to implement a relaxed clock using a thorney likelihood? https://
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relaxed clock with thorney likelihood
Hello BEASTies, Anyone know how to implement a relaxed clock using a thorney likelihood? https://
Jun 19
Jimmy A Mcguire
,
higg...@gmail.com
3
Jun 18
StarBeast3 multithreading
Hi Remco, Thanks so much for getting back to me! As it turns out, I figured out my mistake thanks to
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StarBeast3 multithreading
Hi Remco, Thanks so much for getting back to me! As it turns out, I figured out my mistake thanks to
Jun 18