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Alexei Drummond
, …
Master Cheng
19
7/28/19
Announcement
New 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
unread,
Announcement
New 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 Drummond
2
5/1/19
Announcement
6th 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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Announcement
6th 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 Drummond
2
11/1/16
Announcement
Workshop 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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Announcement
Workshop 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
Bingying Li
Jun 21
Low ESS values for some parameters
Hi everyone, I am running a nucleotide dataset of the influenza HA gene with ~1300 sequences, 4
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Low ESS values for some parameters
Hi everyone, I am running a nucleotide dataset of the influenza HA gene with ~1300 sequences, 4
Jun 21
Daniel Eusebio Quintero Vallejo
,
Jordan Douglas
4
Jun 19
Justifying lognormal priors in BEAST
Hi Daniel, Personally, I don't think that offsets (or minimums or maximums) are appropriate in
unread,
Justifying lognormal priors in BEAST
Hi Daniel, Personally, I don't think that offsets (or minimums or maximums) are appropriate in
Jun 19
Daniel Eusebio Quintero Vallejo
Jun 19
Using uniform priors for root calibration and enforcing monophyly
Dear all, I'm working on a time-calibrated phylogenetic analysis using BEAST, and I'd
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Using uniform priors for root calibration and enforcing monophyly
Dear all, I'm working on a time-calibrated phylogenetic analysis using BEAST, and I'd
Jun 19
Shoaib Khan
,
Jordan Douglas
2
Jun 19
Inquiry Regarding Amino Acid Sequence Support in BEAST
Dear Shoaib, Yes BEAST 2 and BEAST X both support amino acids, using substitution models like
unread,
Inquiry Regarding Amino Acid Sequence Support in BEAST
Dear Shoaib, Yes BEAST 2 and BEAST X both support amino acids, using substitution models like
Jun 19
Shoaib Khan
Jun 19
Protein Sequence Example and Errors While Uploading Nexus File
Dear BEAST Team, I am currently working on phylogenetic analysis using protein (amino acid) sequences
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Protein Sequence Example and Errors While Uploading Nexus File
Dear BEAST Team, I am currently working on phylogenetic analysis using protein (amino acid) sequences
Jun 19
Hee Han
Jun 19
Why does beast shut down?
Hi everyone, My beast always shuts down while it works. This phenomenon only occurred when I
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Why does beast shut down?
Hi everyone, My beast always shuts down while it works. This phenomenon only occurred when I
Jun 19
Abhishek Gupta
, …
Abhishek Gupta
7
Jun 16
About the clock mean value
Thanks for fruitful replies. i have one more doubt as i am running beast to know TMRCA for 5
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About the clock mean value
Thanks for fruitful replies. i have one more doubt as i am running beast to know TMRCA for 5
Jun 16
cmh
, …
Artem B
3
Jun 11
Error at the beginning of stepping stone sampling when using UCLN/Skygrid or Strict/Skygrid combinations
Hey Mateusz, As I remember, SkyGrid has improper priors which do not integrate to 1, so the error can
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Error at the beginning of stepping stone sampling when using UCLN/Skygrid or Strict/Skygrid combinations
Hey Mateusz, As I remember, SkyGrid has improper priors which do not integrate to 1, so the error can
Jun 11
Diego Caraballo
, …
higg...@gmail.com
5
Jun 9
Significant tree length change in TreeParser
OK, just make sure to check that the tip dates in the trees that are sampled are correct. Remco On
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Significant tree length change in TreeParser
OK, just make sure to check that the tip dates in the trees that are sampled are correct. Remco On
Jun 9
Terry Jones
, …
Camila Duitama
9
Jun 6
Python for generating BEAST2 XML files
Hi! I am new to BEAST, and I will be conducting numerous experiments and replicates; therefore, I
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Python for generating BEAST2 XML files
Hi! I am new to BEAST, and I will be conducting numerous experiments and replicates; therefore, I
Jun 6
Robert Yuan
,
higg...@gmail.com
3
Jun 6
Generalized stepping-stone in BEAST2?
Dear Remco, Thank you for clarifying. I was interested in the latter - in that case I'll stick to
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Generalized stepping-stone in BEAST2?
Dear Remco, Thank you for clarifying. I was interested in the latter - in that case I'll stick to
Jun 6
Jaume Ros
Jun 4
Error in BEAUti: getParent() is null when generating XML from concatenated amino acid alignment
Dear colleagues, I'm encountering an error in BEAUti v10.5.0 when trying to generate an XML file
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Error in BEAUti: getParent() is null when generating XML from concatenated amino acid alignment
Dear colleagues, I'm encountering an error in BEAUti v10.5.0 when trying to generate an XML file
Jun 4
Hee Han
Jun 1
Discordance of starting newick tree and beast results
Hi everyone, I am trying to make a beast tree using an ML result. I use the Starting tree panel and
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Discordance of starting newick tree and beast results
Hi everyone, I am trying to make a beast tree using an ML result. I use the Starting tree panel and
Jun 1
Dylan O'Hearn
May 26
Skyline Interpretation
Hello, I'm analyzing a small wildlife population (7 individuals all collected from within a few
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Skyline Interpretation
Hello, I'm analyzing a small wildlife population (7 individuals all collected from within a few
May 26
Dylan O'Hearn
May 24
Ploidy in Starbeast and EBSP
Hello, When using phased haplotypes (ie, the two haplotypes of a nuclear locus in a diploid
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Ploidy in Starbeast and EBSP
Hello, When using phased haplotypes (ie, the two haplotypes of a nuclear locus in a diploid
May 24
Malithi De Silva
,
Artem B
2
May 23
Beast tempest slope is always 1
Hi Malithi, You force R2 to 1 by dating tips in BEAST, which, as far as I understand, fits distances
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Beast tempest slope is always 1
Hi Malithi, You force R2 to 1 by dating tips in BEAST, which, as far as I understand, fits distances
May 23
Sunny Beckham
May 23
Seeking BEAST2 help or consultant for linguistic phylogeny project
Hi all, I'm building a BEAST2 analysis using linguistic data (binary character matrix) and tip-
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Seeking BEAST2 help or consultant for linguistic phylogeny project
Hi all, I'm building a BEAST2 analysis using linguistic data (binary character matrix) and tip-
May 23
Victor Lundström
May 23
substitution model: birth-death model
Hi, Does anyone have any literature recommendation for the mutation-death model in beauti? I would
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substitution model: birth-death model
Hi, Does anyone have any literature recommendation for the mutation-death model in beauti? I would
May 23
Michael Martin
May 20
SkyGrid plots in tracer
Hi all, I'm working with a Skygrid coalescent model and have some questions about the Ne
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SkyGrid plots in tracer
Hi all, I'm working with a Skygrid coalescent model and have some questions about the Ne
May 20
Mihajlo Milic
May 18
ESS of multiple BEAST runs
Dear group members, I have run several independent MCMC runs in the BEAST to check for the
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ESS of multiple BEAST runs
Dear group members, I have run several independent MCMC runs in the BEAST to check for the
May 18
Mihajlo Milic
May 18
Individual and combined ESS issue
Dear group members, I ran several independent MCC runs in the BEAST to check for the convergence
unread,
Individual and combined ESS issue
Dear group members, I ran several independent MCC runs in the BEAST to check for the convergence
May 18
David Lohman
May 13
gtr.rates and frequencies for a single partition flatline in independent analyses
Greetings, I'm running a BEAST dating analysis with 197 taxa and 100 loci in 16 partitions. The
unread,
gtr.rates and frequencies for a single partition flatline in independent analyses
Greetings, I'm running a BEAST dating analysis with 197 taxa and 100 loci in 16 partitions. The
May 13
Dylan O'Hearn
, …
Luke Baton
12
May 9
Speedemon/Stacey collapse height
Thanks for taking the trouble to explain things, Bengt. OK, we agree about, and have the same
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Speedemon/Stacey collapse height
Thanks for taking the trouble to explain things, Bengt. OK, we agree about, and have the same
May 9
Bruno Alves Sousa Coelho
,
Artem B
3
May 6
Help with low values for prior and posterior
Hi Bruno, The traces of ucldMean and sigma should be checked in the first place. It would be good to
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Help with low values for prior and posterior
Hi Bruno, The traces of ucldMean and sigma should be checked in the first place. It would be good to
May 6
luca gregnanin
May 5
Class could not be found - SNAPPER analysis
Dear BEAST users, I'm carrying out a dated phylogenetic analysis with SNAPPER. I installed BEAST
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Class could not be found - SNAPPER analysis
Dear BEAST users, I'm carrying out a dated phylogenetic analysis with SNAPPER. I installed BEAST
May 5
Lahn Serio
, …
ac.a...@gmail.com
3
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 Brina
8
Apr 23
Unable to import alignment file into Beauti 2
Hi 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 2
Hi Dan. Wow, that's a very big alignment file. So far, based on previous posts here, that command
Apr 23
Jyotishko Koley
,
Artem B
2
Apr 22
Low GTR rate ESS
Hi Jyotishko, Checking the MCMC traces of the rates makes sense. Can you provide a screenshot? Cheers
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Low GTR rate ESS
Hi 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 BEAST2
Hi everyone, I'm trying to run BFD* for species delimitation under scenarios of one, two, three,
unread,
Error when trying to run Bayes Factor Delimitation (BFD*) via SNAPP in BEAST2
Hi everyone, I'm trying to run BFD* for species delimitation under scenarios of one, two, three,
Apr 21
Jo Baker
,
Omar Idris
3
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
unread,
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