beast-users - Google Groups (original) (raw)
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Alexei Drummond, … Master Cheng19
7/28/19
AnnouncementNew version of StarBEAST2 (v0.13)Dear Tim I want to know how to resume the analyze in Beast2,Could you sent me the relation the
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AnnouncementNew version of StarBEAST2 (v0.13)Dear Tim I want to know how to resume the analyze in Beast2,Could you sent me the relation the
7/28/19
Alexei Drummond2
5/1/19
Announcement6th Taming the BEAST workshop in beautiful Squamish, British Columbia (August 12-16 2019)Applications are now closed. We have a few places left so late applications will be considered on a
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Announcement6th Taming the BEAST workshop in beautiful Squamish, British Columbia (August 12-16 2019)Applications are now closed. We have a few places left so late applications will be considered on a
5/1/19
Alexei Drummond2
11/1/16
AnnouncementWorkshop Announcement: Taming the BEAST in the South Pacific!This is the final call for Taming the BEAST in the South Pacific, a 5-day summer short course on
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AnnouncementWorkshop Announcement: Taming the BEAST in the South Pacific!This is the final call for Taming the BEAST in the South Pacific, a 5-day summer short course on
11/1/16
cmh, Mateusz Baca2
Apr 29
Error at the beginning of stepping stone sampling when using UCLN/Skygrid or Strict/Skygrid combinationsHi Crystal, I was wondering if you have received any responses or found a workaround? I am
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Error at the beginning of stepping stone sampling when using UCLN/Skygrid or Strict/Skygrid combinationsHi Crystal, I was wondering if you have received any responses or found a workaround? I am
Apr 29
Bruno Alves Sousa Coelho2
Apr 29
Help with low values for prior and posteriorJust adding pictures of the log files in tracer Em terça-feira, 29 de abril de 2025 às 00:05:36 UTC-3
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Help with low values for prior and posteriorJust adding pictures of the log files in tracer Em terça-feira, 29 de abril de 2025 às 00:05:36 UTC-3
Apr 29
Lahn Serio, … ac.a...@gmail.com3
Apr 24
BEAUTI: Could not get an internet connection.Had same issue. Downloading the package and extracting in a folder with same name in ~/.beast/2.7/
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BEAUTI: Could not get an internet connection.Had same issue. Downloading the package and extracting in a folder with same name in ~/.beast/2.7/
Apr 24
Antonio Galán Sánchez, … Mamerto Brina8
Apr 23
Unable to import alignment file into Beauti 2Hi Dan. Wow, that's a very big alignment file. So far, based on previous posts here, that command
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Unable to import alignment file into Beauti 2Hi Dan. Wow, that's a very big alignment file. So far, based on previous posts here, that command
Apr 23
Jyotishko Koley, Artem B2
Apr 22
Low GTR rate ESSHi Jyotishko, Checking the MCMC traces of the rates makes sense. Can you provide a screenshot? Cheers
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Low GTR rate ESSHi Jyotishko, Checking the MCMC traces of the rates makes sense. Can you provide a screenshot? Cheers
Apr 22
Gabriel Monteiro de Lima
Apr 21
Error when trying to run Bayes Factor Delimitation (BFD*) via SNAPP in BEAST2Hi everyone, I'm trying to run BFD* for species delimitation under scenarios of one, two, three,
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Error when trying to run Bayes Factor Delimitation (BFD*) via SNAPP in BEAST2Hi everyone, I'm trying to run BFD* for species delimitation under scenarios of one, two, three,
Apr 21
Jo Baker, Omar Idris3
Apr 19
Returning specific tip dates in logs (FBD+SA)Sorry I'm not sure I understand what you mean. Have you managed to identify what id would be need
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Returning specific tip dates in logs (FBD+SA)Sorry I'm not sure I understand what you mean. Have you managed to identify what id would be need
Apr 19
nicolas hazzi
Apr 17
Path marginal likelihood issueHi everyone, I am trying to run on a Windows laptop, a path analysis to then used the marginal
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Path marginal likelihood issueHi everyone, I am trying to run on a Windows laptop, a path analysis to then used the marginal
Apr 17
Omar Idris
Apr 16
Re: TreeAnnotator MCC Low Posterior ProbabilitiesAre you constraining too much using your MRCA fossil priors try to reduce may be. ONI On Tue, Apr 8,
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Re: TreeAnnotator MCC Low Posterior ProbabilitiesAre you constraining too much using your MRCA fossil priors try to reduce may be. ONI On Tue, Apr 8,
Apr 16
Gabriel Monteiro de Lima
Apr 16
Question about computational time for completing a SNAPP runHi everyone, I'd like to ask a question—I've recently started using BEAST2. I'm trying to
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Question about computational time for completing a SNAPP runHi everyone, I'd like to ask a question—I've recently started using BEAST2. I'm trying to
Apr 16
Kritchakorn Sawakwongpra, … Alexei Drummond7
Apr 8
Substitution and site models of RNA virusThank you for all suggestion. On Tuesday, January 21, 2025 at 3:44:14 AM UTC+7 Alexei Drummond wrote:
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Substitution and site models of RNA virusThank you for all suggestion. On Tuesday, January 21, 2025 at 3:44:14 AM UTC+7 Alexei Drummond wrote:
Apr 8
Kritchakorn Sawakwongpra
Apr 8
Assessing Clock model for RNA virusHello everyone, I would like to consult with you regarding model selection for Norovirus ( RNA virus)
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Assessing Clock model for RNA virusHello everyone, I would like to consult with you regarding model selection for Norovirus ( RNA virus)
Apr 8
Patricia Torres, Jordan Douglas6
Apr 8
Error BEAST2 SNAPPER+SPEEDEMONThank you for your insights, Jordan. The extra space is not in the actual alignment, it might have
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Error BEAST2 SNAPPER+SPEEDEMONThank you for your insights, Jordan. The extra space is not in the actual alignment, it might have
Apr 8
Ziv Lieberman, higg...@gmail.com3
Apr 1
Dirichlet prior on exchangeabilities?Hi Remco, Thank you so much for your insight! I will try out this implementation of priors. Cheers, -
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Dirichlet prior on exchangeabilities?Hi Remco, Thank you so much for your insight! I will try out this implementation of priors. Cheers, -
Apr 1
Sikandar Azam, … Pfeiffer, Wayne4
Apr 1
Optimizing BEAST Runs for Large Datasets (1000-1500 Sequences, >15kb)Hi Sikandar, You should try using your GPU with BEAGLE. Best regards, Wayne On Mar 31, 2025, at 10:27
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Optimizing BEAST Runs for Large Datasets (1000-1500 Sequences, >15kb)Hi Sikandar, You should try using your GPU with BEAGLE. Best regards, Wayne On Mar 31, 2025, at 10:27
Apr 1
Opeyemi Alayande, Artem B9
Mar 30
Assessing Temporal Signal and Clock Model Selection in Mtb WGS DataThank you very much Artem for providing these details. Sincere appreciation On Friday, 28 March 2025
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Assessing Temporal Signal and Clock Model Selection in Mtb WGS DataThank you very much Artem for providing these details. Sincere appreciation On Friday, 28 March 2025
Mar 30
bengt....@gmail.com, … Jordan Douglas6
Mar 29
Setting upp a StarBeast analysis with species traitsHi, Regarding the speed of starbeast3 - are you referring to the computation time (states logged per
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Setting upp a StarBeast analysis with species traitsHi, Regarding the speed of starbeast3 - are you referring to the computation time (states logged per
Mar 29
Mark Hanson, … Omar Idris5
Mar 27
BEAST tree not reading as ultrametric in R - but it isThanks for response. Tree made in BEAST, loaded in then exported from FigTree, then loaded in R.
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BEAST tree not reading as ultrametric in R - but it isThanks for response. Tree made in BEAST, loaded in then exported from FigTree, then loaded in R.
Mar 27
Katherin Hinojosa, Omar Mejía2
Mar 26
LogcombinerWhat kind of files you are trying to merge? Will be better if you upload your files, otherwise its
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LogcombinerWhat kind of files you are trying to merge? Will be better if you upload your files, otherwise its
Mar 26
Giske Lagerweij, Tim Vaughan4
Mar 26
Why is there option for estimating kappa in the BDMM / Multitype tree packageHi Giske, I'm afraid not - the latest MTT release is intended to work with the latest BEAST 2
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Why is there option for estimating kappa in the BDMM / Multitype tree packageHi Giske, I'm afraid not - the latest MTT release is intended to work with the latest BEAST 2
Mar 26
Prapti Satpathy, Joëlle Barido-Sottani2
Mar 25
ClaDS on a dated treeHello Prapti, Yes, you can absolutely run ClaDS directly from the tree. The easiest way to set it up
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ClaDS on a dated treeHello Prapti, Yes, you can absolutely run ClaDS directly from the tree. The easiest way to set it up
Mar 25
CJ Battey, … Jacopo Franzoni24
Mar 23
error with BEAST2.2.0 SNAPP+MODEL_SELECTIONHi Nichelle, I tried solution B but I still obtain the same error. I dont understand the solution A.
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error with BEAST2.2.0 SNAPP+MODEL_SELECTIONHi Nichelle, I tried solution B but I still obtain the same error. I dont understand the solution A.
Mar 23
Diego Caraballo
Mar 18
Significant tree length change in TreeParserHi everyone, I am running a speedemon species delimitation analysis in which I entered a starting
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Significant tree length change in TreeParserHi everyone, I am running a speedemon species delimitation analysis in which I entered a starting
Mar 18
Hee Han
Mar 11
Newick Starting Tree Error?Dear beast users, I am currently trying to estimate the time divergence calibration with beauti and
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Newick Starting Tree Error?Dear beast users, I am currently trying to estimate the time divergence calibration with beauti and
Mar 11
victor piñon, … Gustavo Ballen4
Mar 11
Topology issuesHi, Sorry for the late response, I was waiting to get the new tree to see if everything was working
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Topology issuesHi, Sorry for the late response, I was waiting to get the new tree to see if everything was working
Mar 11
Diego Caraballo
Mar 10
SNAPPER - Are linked loci desirable?Hi everybody! I've been thinking about the usefulness of using linked SNPs and would like your
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SNAPPER - Are linked loci desirable?Hi everybody! I've been thinking about the usefulness of using linked SNPs and would like your
Mar 10
Thomas vG
Mar 9
General Questions About the Inner Workings of BEAST/SPREAD3 Regarding the Calculated Origin of Viral OutbreaksHello everyone I am working with viral whole genome data (all sampled from the same year) and wanted
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General Questions About the Inner Workings of BEAST/SPREAD3 Regarding the Calculated Origin of Viral OutbreaksHello everyone I am working with viral whole genome data (all sampled from the same year) and wanted
Mar 9
Lily Hughes, Kieran Althaus5
Mar 5
Unable to turn off topology search in BEAST 2.7.7?Yes! It took me a while, but I figured it out. I think some of the documentation has lagged behind
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Unable to turn off topology search in BEAST 2.7.7?Yes! It took me a while, but I figured it out. I think some of the documentation has lagged behind
Mar 5
Antonio Galán Sánchez
Mar 4
Error 110 Parsing the xml input file (active/inactive nodes)Dear all, I have been trying to run a divergence time analysis on a UCE data matrix (25% occupancy)
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Error 110 Parsing the xml input file (active/inactive nodes)Dear all, I have been trying to run a divergence time analysis on a UCE data matrix (25% occupancy)
Mar 4
Ali Al-Rashed
Mar 4
BEAST output files not savingHi everyone, I've tried running 200 mil MCMC BEAST runs but the log and tree files only contain ~
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BEAST output files not savingHi everyone, I've tried running 200 mil MCMC BEAST runs but the log and tree files only contain ~
Mar 4