beast-users

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Juliano Comandulli, higg...@gmail.com4

Dec 1

I managed to solve it, I had to download the packages to be able to run what was done. Thanks for

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I managed to solve it, I had to download the packages to be able to run what was done. Thanks for

Dec 1

Nov 30

Is the "height" attribute in metacomments of an annotated tree a height of a node in a target tree?

Hello, everyone I would like to resolve the ambiguity I got with annotated trees. I have noted that

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Is the "height" attribute in metacomments of an annotated tree a height of a node in a target tree?

Hello, everyone I would like to resolve the ambiguity I got with annotated trees. I have noted that

Nov 30

Nov 30

analyses slowing

Hi all, This is a question I have been curious about for awhile. Why do BEAST analyses continue to

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analyses slowing

Hi all, This is a question I have been curious about for awhile. Why do BEAST analyses continue to

Nov 30

Nov 30

Cannot load alignment file in BEAUti

Looks like I needed to close and restart BEAUti. This fixed the problem. On Wednesday, 30 November

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Cannot load alignment file in BEAUti

Looks like I needed to close and restart BEAUti. This fixed the problem. On Wednesday, 30 November

Nov 30

Nov 30

question about ESS value

Hi lovely ppl! i've made 2 indenpendent run of then datesite and all ESS values are >200.

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question about ESS value

Hi lovely ppl! i've made 2 indenpendent run of then datesite and all ESS values are >200.

Nov 30

Nov 30

different modle with different posterior probability

hi! Bei's here i've tried both GTR and TN93 model for my datasite. for GTR model it's

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different modle with different posterior probability

hi! Bei's here i've tried both GTR and TN93 model for my datasite. for GTR model it's

Nov 30

Nov 30

TreeAnnotater help!

hi there! i've combined 3 run with two 20millions and one with 50million chain length. The

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TreeAnnotater help!

hi there! i've combined 3 run with two 20millions and one with 50million chain length. The

Nov 30

Dylan O'Hearn, … Pei-Wei Sun12

Nov 29

StarBeast 2 Clock Rates

Hello Jordan I have also encountered this "Eigenvalues not converged for Q-matrix" error

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StarBeast 2 Clock Rates

Hello Jordan I have also encountered this "Eigenvalues not converged for Q-matrix" error

Nov 29

citromicrobium...@gmail.com

Nov 29

run beast using only 4-fold degenerate sites?

Hi, I am wondering whether it would be advisable to run BEAST using only 4-fold degenerate sites (

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run beast using only 4-fold degenerate sites?

Hi, I am wondering whether it would be advisable to run BEAST using only 4-fold degenerate sites (

Nov 29

Palesa Madupe, Jordan Douglas2

Nov 28

Error 1017 parsing the xml input file ---BEAST v 2.6.7

Hi Palesa, That is very strange. starbeast2 or 3 should be the only dependencies. Perhaps the package

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Error 1017 parsing the xml input file ---BEAST v 2.6.7

Hi Palesa, That is very strange. starbeast2 or 3 should be the only dependencies. Perhaps the package

Nov 28

Nov 27

Error when using BEASTGen

Hi all, I am attempting to extract data from XML files (morphological characters as well as sequence

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Error when using BEASTGen

Hi all, I am attempting to extract data from XML files (morphological characters as well as sequence

Nov 27

Robin Cristofari, … Naoki Takebayashi6

Nov 23

Running Beast2 on Fedora 27

This is an old thread, but I came to this problem with BEAST 2.6.7 with Fedora 35. I'm posting

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Running Beast2 on Fedora 27

This is an old thread, but I came to this problem with BEAST 2.6.7 with Fedora 35. I'm posting

Nov 23

Dylan O'Hearn, higg...@gmail.com2

Nov 23

Launching Beast 2.7.x from command line

Hi Dylan, This is a bug and I created an issue for it (#1063). It appears that when many packages (24

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Launching Beast 2.7.x from command line

Hi Dylan, This is a bug and I created an issue for it (#1063). It appears that when many packages (24

Nov 23

zhijian zhou, Brandon Stark2

Nov 21

Increase the sampling frequency

hi, decrease the value. 在2022年11月14日星期一 UTC+8 02:35:17<zhouzh...@gmail.com> 写道： Sorry to bother

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Increase the sampling frequency

hi, decrease the value. 在2022年11月14日星期一 UTC+8 02:35:17<zhouzh...@gmail.com> 写道： Sorry to bother

Nov 21

hojoun Jeong, … Omar Idris9

Nov 16

My effective population size too large in BSP

0.034 in my or .034e-6 in years? not confident myself as it gave me branch lengths in the order of e6

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My effective population size too large in BSP

0.034 in my or .034e-6 in years? not confident myself as it gave me branch lengths in the order of e6

Nov 16

Dylan O'Hearn, Alexei Drummond2

Nov 16

Starbeast3 with phased nuclear and mitochondrial dna

I believe that If you are including both parental copies (or one from a random parent) of the diploid

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Starbeast3 with phased nuclear and mitochondrial dna

I believe that If you are including both parental copies (or one from a random parent) of the diploid

Nov 16

George Gao, … Yeserin YILDIRIM4

Nov 16

Error 1017 parsing the xml input file ---BEAST v 2.6.1

Hi Remco, I have the same problem. Trying to run snapper. Prepared the input file using snapp_prep.rb

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Error 1017 parsing the xml input file ---BEAST v 2.6.1

Hi Remco, I have the same problem. Trying to run snapper. Prepared the input file using snapp_prep.rb

Nov 16

Jose Ramirezs, HS3

Nov 16

Different topology from starting tree

Hi Hovhanne, Thank you for your answer, Yes, the operators (Wide-exchange, Narrow-exchange, Wilson-

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Different topology from starting tree

Hi Hovhanne, Thank you for your answer, Yes, the operators (Wide-exchange, Narrow-exchange, Wilson-

Nov 16

Gabriela Cruz Luna, … Omar Idris7

Nov 15

Help with TreeAnnotator

Thank you for your email Alexei. Omar On Tue, Nov 15, 2022 at 8:11 PM Alexei Drummond <alexei.

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Help with TreeAnnotator

Thank you for your email Alexei. Omar On Tue, Nov 15, 2022 at 8:11 PM Alexei Drummond <alexei.

Nov 15

Dylan O'Hearn, Alexei Drummond2

Nov 13

The use of outgroups

The main problem with outgroups: the way they are selected and sampled is usually inconsistent with

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The use of outgroups

The main problem with outgroups: the way they are selected and sampled is usually inconsistent with

Nov 13

Nov 13

Multiple Monophyletic Constraint doesn't work

Hi, I'm trying to run BEAST (v2.7.2) with a multiple monophyletic constraint, but I keep

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Multiple Monophyletic Constraint doesn't work

Hi, I'm trying to run BEAST (v2.7.2) with a multiple monophyletic constraint, but I keep

Nov 13

Nov 13

running bayesian analysis in BEAST

Dear Beast users, I want to run simple Bayesian analysis (not divergence time estimation) in Beast to

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running bayesian analysis in BEAST

Dear Beast users, I want to run simple Bayesian analysis (not divergence time estimation) in Beast to

Nov 13

Nov 13

treeModel.rootHeight in BEAST2

Hi, I would like to calibrate the root height of a tree using fossil information. But while in Beast

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treeModel.rootHeight in BEAST2

Hi, I would like to calibrate the root height of a tree using fossil information. But while in Beast

Nov 13

Nov 13

rootModel.rootHeight in BEAST2

Hi, I would like to calibrate the root height of a tree using fossil information. But while in Beast

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rootModel.rootHeight in BEAST2

Hi, I would like to calibrate the root height of a tree using fossil information. But while in Beast

Nov 13

PILAR POZO PIÑOL

Nov 13

Error message when running MASCOT in Beast2

Hi, I am trying to run samples from different animal species using MASCOT. However, I got this

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Error message when running MASCOT in Beast2

Hi, I am trying to run samples from different animal species using MASCOT. However, I got this

Nov 13

Nov 13

Running Bayesian analysis in Beast

Dear Beast users, I want to run simple Bayesian analysis (not divergence time estimation) in Beast to

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Running Bayesian analysis in Beast

Dear Beast users, I want to run simple Bayesian analysis (not divergence time estimation) in Beast to

Nov 13

Nov 13

Interpreting Tracer output - turnoverFBD - FBD divergence time estimation

Hi all, I'm using BEAST v2 to estimate divergence time using the FBD process from a dataset that

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Interpreting Tracer output - turnoverFBD - FBD divergence time estimation

Hi all, I'm using BEAST v2 to estimate divergence time using the FBD process from a dataset that

Nov 13

PRINCE KUMAR SAH2

Nov 13

Re: Error: Fatal exception: Could not find a proper state to initialise. Perhaps try another seed

Dear All, I have generated an XML file, which I tried to run in beast 2, but I am getting the

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Re: Error: Fatal exception: Could not find a proper state to initialise. Perhaps try another seed

Dear All, I have generated an XML file, which I tried to run in beast 2, but I am getting the

Nov 13

Cherry Mae Labrador

Nov 13

A fatal error has been detected by the Java Runtime Environment

Hi Everybody, Could you help me solve this? I've been trying to use Beast. However, I keep

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A fatal error has been detected by the Java Runtime Environment

Hi Everybody, Could you help me solve this? I've been trying to use Beast. However, I keep

Nov 13

Nov 13

Extracting posterior ages of nodes from beast outputs, to graph distributions

I would like to create density graphs of the posterior/marginal prior resulting from divergence time

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Extracting posterior ages of nodes from beast outputs, to graph distributions

I would like to create density graphs of the posterior/marginal prior resulting from divergence time

Nov 13

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