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beast...@googlecode.com

4/14/15

Issue 763 in beast-mcmc: BEAUti creates a subtree slide operator with size zero when data is invariable

Status: Accepted Owner: ramb...@gmail.com Labels: Type-Defect Priority-Medium BEAUti v1.8.2 Milestone

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Issue 763 in beast-mcmc: BEAUti creates a subtree slide operator with size zero when data is invariable

Status: Accepted Owner: ramb...@gmail.com Labels: Type-Defect Priority-Medium BEAUti v1.8.2 Milestone

4/14/15

beast...@googlecode.com

4/3/15

Issue 762 in beast-mcmc: Spurious <coalescentEventsStatistic> block inserted in log when selecting skygrid

Status: New Owner: ---- Labels: Type-Defect Priority-Medium New issue 762 by luizepid...@gmail.com:

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Issue 762 in beast-mcmc: Spurious <coalescentEventsStatistic> block inserted in log when selecting skygrid

Status: New Owner: ---- Labels: Type-Defect Priority-Medium New issue 762 by luizepid...@gmail.com:

4/3/15

beast...@googlecode.com

3/30/15

Issue 761 in beast-mcmc: Tracer BSP plots missing 10^-1 labels

Status: New Owner: ramb...@gmail.com Labels: Type-Defect Priority-Medium Tracer 1.6 Milestone-

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Issue 761 in beast-mcmc: Tracer BSP plots missing 10^-1 labels

Status: New Owner: ramb...@gmail.com Labels: Type-Defect Priority-Medium Tracer 1.6 Milestone-

3/30/15

beast...@googlecode.com9

3/27/15

Issue 750 in beast-mcmc: -Infinity value always come out when i try to load xml

Comment #8 on issue 750 by ramb...@gmail.com: -Infinity value always come out when i try to load xml

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Issue 750 in beast-mcmc: -Infinity value always come out when i try to load xml

Comment #8 on issue 750 by ramb...@gmail.com: -Infinity value always come out when i try to load xml

3/27/15

beast...@googlecode.com

3/12/15

Issue 760 in beast-mcmc: Export project to Github or another repo host

Status: New Owner: ramb...@gmail.com Labels: Type-Task Priority-High New issue 760 by Sibon...@gmail.

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Issue 760 in beast-mcmc: Export project to Github or another repo host

Status: New Owner: ramb...@gmail.com Labels: Type-Task Priority-High New issue 760 by Sibon...@gmail.

3/12/15

beast...@googlecode.com3

3/5/15

Issue 745 in beast-mcmc: Removing an HPM from some parameters doesn't remove the model in the XML

Updates: Labels: -Milestone-Release1.8.1 Milestone-Release1.8.2 Comment #2 on issue 745 by ramb...@

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Issue 745 in beast-mcmc: Removing an HPM from some parameters doesn't remove the model in the XML

Updates: Labels: -Milestone-Release1.8.1 Milestone-Release1.8.2 Comment #2 on issue 745 by ramb...@

3/5/15

beast...@googlecode.com3

3/5/15

Issue 747 in beast-mcmc: Duplicate references in robust counting with multiple partitions

Updates: Labels: beauti v1.8.1 Milestone-Release1.8.2 Comment #2 on issue 747 by ramb...@gmail.com:

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Issue 747 in beast-mcmc: Duplicate references in robust counting with multiple partitions

Updates: Labels: beauti v1.8.1 Milestone-Release1.8.2 Comment #2 on issue 747 by ramb...@gmail.com:

3/5/15

beast...@googlecode.com2

3/5/15

Issue 731 in beast-mcmc: -seed option for MC3

Updates: Status: WontFix Comment #1 on issue 731 by ramb...@gmail.com: -seed option for MC3 https://

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Issue 731 in beast-mcmc: -seed option for MC3

Updates: Status: WontFix Comment #1 on issue 731 by ramb...@gmail.com: -seed option for MC3 https://

3/5/15

beast...@googlecode.com2

3/5/15

Issue 717 in beast-mcmc: Tracer not rescaling trace plot for multiple traces

Updates: Labels: -Milestone-Release1.6.1 Milestone-Release1.7 Comment #1 on issue 717 by ramb...@

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Issue 717 in beast-mcmc: Tracer not rescaling trace plot for multiple traces

Updates: Labels: -Milestone-Release1.6.1 Milestone-Release1.7 Comment #1 on issue 717 by ramb...@

3/5/15

beast...@googlecode.com3

3/5/15

Issue 711 in beast-mcmc: Sum constraints for Dirichlet distribution

Updates: Labels: -Milestone-Release1.8.2 Milestone-Release1.9 Comment #2 on issue 711 by ramb...@

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Issue 711 in beast-mcmc: Sum constraints for Dirichlet distribution

Updates: Labels: -Milestone-Release1.8.2 Milestone-Release1.9 Comment #2 on issue 711 by ramb...@

3/5/15

beast...@googlecode.com3

3/5/15

Issue 686 in beast-mcmc: Logistic growth shape vs t50

Updates: Labels: -Milestone-Release1.6 Milestone-Release1.7 Comment #2 on issue 686 by ramb...@gmail.

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Issue 686 in beast-mcmc: Logistic growth shape vs t50

Updates: Labels: -Milestone-Release1.6 Milestone-Release1.7 Comment #2 on issue 686 by ramb...@gmail.

3/5/15

beast...@googlecode.com3

3/5/15

Re: Issue 648 in beast-mcmc: If you log a multivariate trait for a node to a log file then it is enclosed in curly braces

Updates: Labels: -Milestone-Release1.8 Milestone-Release1.9 Comment #4 on issue 648 by ramb...@gmail.

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Re: Issue 648 in beast-mcmc: If you log a multivariate trait for a node to a log file then it is enclosed in curly braces

Updates: Labels: -Milestone-Release1.8 Milestone-Release1.9 Comment #4 on issue 648 by ramb...@gmail.

3/5/15

beast...@googlecode.com

3/5/15

Re: Issue 613 in beast-mcmc: CodonPartitionedRobustCounting gives Array Out Of Bounds Exception if codon position pattern lists are different sizes

Updates: Labels: -Milestone-Release1.8 Milestone-Release1.9 Comment #1 on issue 613 by ramb...@gmail.

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Re: Issue 613 in beast-mcmc: CodonPartitionedRobustCounting gives Array Out Of Bounds Exception if codon position pattern lists are different sizes

Updates: Labels: -Milestone-Release1.8 Milestone-Release1.9 Comment #1 on issue 613 by ramb...@gmail.

3/5/15

beast...@googlecode.com

3/5/15

Re: Issue 366 in beast-mcmc: BEAUti needs to read trait information when importing XMLs

Updates: Labels: -Milestone-Release1.8 Milestone-Release1.9 Comment #4 on issue 366 by ramb...@gmail.

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Re: Issue 366 in beast-mcmc: BEAUti needs to read trait information when importing XMLs

Updates: Labels: -Milestone-Release1.8 Milestone-Release1.9 Comment #4 on issue 366 by ramb...@gmail.

3/5/15

beast...@googlecode.com

3/5/15

Re: Issue 329 in beast-mcmc: Suggest a standard demographic log file format

Updates: Labels: -Milestone-Release1.8 Milestone-Release1.9 Comment #5 on issue 329 by ramb...@gmail.

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Re: Issue 329 in beast-mcmc: Suggest a standard demographic log file format

Updates: Labels: -Milestone-Release1.8 Milestone-Release1.9 Comment #5 on issue 329 by ramb...@gmail.

3/5/15

beast...@googlecode.com2

3/5/15

Re: Issue 177 in beast-mcmc: BEAUTi: a new Summary tab panel

Updates: Labels: -Milestone-Release1.8 Milestone-Release1.9 Comment #3 on issue 177 by ramb...@gmail.

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Re: Issue 177 in beast-mcmc: BEAUTi: a new Summary tab panel

Updates: Labels: -Milestone-Release1.8 Milestone-Release1.9 Comment #3 on issue 177 by ramb...@gmail.

3/5/15

beast...@googlecode.com6

3/5/15

Issue 738 in beast-mcmc: Beauti not retaining settings when saved file is reopened.

Updates: Labels: -Milestone-Release1.8.2 Milestone-Release1.9 Comment #5 on issue 738 by ramb...@

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Issue 738 in beast-mcmc: Beauti not retaining settings when saved file is reopened.

Updates: Labels: -Milestone-Release1.8.2 Milestone-Release1.9 Comment #5 on issue 738 by ramb...@

3/5/15

beast...@googlecode.com3

3/5/15

Issue 748 in beast-mcmc: TreeAnnotator: Sum of clade credibility score for tree reported wrongly when burnin is == 0

Updates: Status: WontFix Comment #2 on issue 748 by ramb...@gmail.com: TreeAnnotator: Sum of clade

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Issue 748 in beast-mcmc: TreeAnnotator: Sum of clade credibility score for tree reported wrongly when burnin is == 0

Updates: Status: WontFix Comment #2 on issue 748 by ramb...@gmail.com: TreeAnnotator: Sum of clade

3/5/15

beast...@googlecode.com6

3/5/15

Issue 751 in beast-mcmc: Full evaluation error

Comment #5 on issue 751 by ramb...@gmail.com: Full evaluation error https://code.google.com/p/beast-

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Issue 751 in beast-mcmc: Full evaluation error

Comment #5 on issue 751 by ramb...@gmail.com: Full evaluation error https://code.google.com/p/beast-

3/5/15

beast...@googlecode.com2

3/5/15

Issue 759 in beast-mcmc: 4 taxa were in the xml file but error messages of "Tree with fewer than 3 taxa" by BEAST

Updates: Labels: -Priority-Medium Priority-Low Comment #1 on issue 759 by ramb...@gmail.com: 4 taxa

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Issue 759 in beast-mcmc: 4 taxa were in the xml file but error messages of "Tree with fewer than 3 taxa" by BEAST

Updates: Labels: -Priority-Medium Priority-Low Comment #1 on issue 759 by ramb...@gmail.com: 4 taxa

3/5/15

beast...@googlecode.com2

2/3/15

Issue 754 in beast-mcmc: BEAST v1.8.1 is not terminating leaving 'zombie' processes

Updates: Status: Fixed Comment #1 on issue 754 by ramb...@gmail.com: BEAST v1.8.1 is not terminating

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Issue 754 in beast-mcmc: BEAST v1.8.1 is not terminating leaving 'zombie' processes

Updates: Status: Fixed Comment #1 on issue 754 by ramb...@gmail.com: BEAST v1.8.1 is not terminating

2/3/15

beast...@googlecode.com4

2/3/15

Issue 756 in beast-mcmc: FEE with random local clock + codon position partitions + multiple threads

Updates: Status: Fixed Comment #3 on issue 756 by ramb...@gmail.com: FEE with random local clock +

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Issue 756 in beast-mcmc: FEE with random local clock + codon position partitions + multiple threads

Updates: Status: Fixed Comment #3 on issue 756 by ramb...@gmail.com: FEE with random local clock +

2/3/15

beast...@googlecode.com

2/3/15

Issue 758 in beast-mcmc: BEAUti multi-partition models turning on state reconstruction

Status: Accepted Owner: ramb...@gmail.com Labels: Type-Defect Priority-Medium beauti v1.8.1 Milestone

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Issue 758 in beast-mcmc: BEAUti multi-partition models turning on state reconstruction

Status: Accepted Owner: ramb...@gmail.com Labels: Type-Defect Priority-Medium beauti v1.8.1 Milestone

2/3/15

beast...@googlecode.com3

2/3/15

Issue 733 in beast-mcmc: Error random local clock

Updates: Status: Duplicate Mergedinto: 756 Comment #2 on issue 733 by ramb...@gmail.com: Error random

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Issue 733 in beast-mcmc: Error random local clock

Updates: Status: Duplicate Mergedinto: 756 Comment #2 on issue 733 by ramb...@gmail.com: Error random

2/3/15

beast...@googlecode.com

2/3/15

Issue 757 in beast-mcmc: Multilocus unlinked relaxed clock models have wrong rate category dimensions

Status: Accepted Owner: ramb...@gmail.com Labels: Type-Defect Priority-Medium beauti v1.8.1 Milestone

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Issue 757 in beast-mcmc: Multilocus unlinked relaxed clock models have wrong rate category dimensions

Status: Accepted Owner: ramb...@gmail.com Labels: Type-Defect Priority-Medium beauti v1.8.1 Milestone

2/3/15

beast...@googlecode.com3

12/23/14

Issue 755 in beast-mcmc: BEAST disappears without error message on running xml BEAUti script

Comment #2 on issue 755 by leonie....@gmail.com: BEAST disappears without error message on running

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Issue 755 in beast-mcmc: BEAST disappears without error message on running xml BEAUti script

Comment #2 on issue 755 by leonie....@gmail.com: BEAST disappears without error message on running

12/23/14

beast...@googlecode.com

12/9/14

Issue 753 in beast-mcmc: Tracer 1.6 has option for categorical data but still won't load non-numerical trace files

Status: Accepted Owner: mdhall272 Labels: Type-Defect Priority-Low Tracer-1.6 New issue 753 by

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Issue 753 in beast-mcmc: Tracer 1.6 has option for categorical data but still won't load non-numerical trace files

Status: Accepted Owner: mdhall272 Labels: Type-Defect Priority-Low Tracer-1.6 New issue 753 by

12/9/14

beast...@googlecode.com2

12/5/14

Issue 749 in beast-mcmc: Multiple partitions with unlinked substitution models can turn on ancestral state reconstruction

Updates: Status: Fixed Comment #1 on issue 749 by ramb...@gmail.com: Multiple partitions with

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Issue 749 in beast-mcmc: Multiple partitions with unlinked substitution models can turn on ancestral state reconstruction

Updates: Status: Fixed Comment #1 on issue 749 by ramb...@gmail.com: Multiple partitions with

12/5/14

beast...@googlecode.com3

11/25/14

Issue 752 in beast-mcmc: i am not able to run beast in Ubuntu server

Comment #2 on issue 752 by aswat...@rgcb.res.in: i am not able to run beast in Ubuntu server https://

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Issue 752 in beast-mcmc: i am not able to run beast in Ubuntu server

Comment #2 on issue 752 by aswat...@rgcb.res.in: i am not able to run beast in Ubuntu server https://

11/25/14

beast...@googlecode.com2

9/6/14

Issue 746 in beast-mcmc: Allows you to have a custom $HOME/lib directory

Updates: Status: Fixed Comment #1 on issue 746 by ramb...@gmail.com: Allows you to have a custom $

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Issue 746 in beast-mcmc: Allows you to have a custom $HOME/lib directory

Updates: Status: Fixed Comment #1 on issue 746 by ramb...@gmail.com: Allows you to have a custom $

9/6/14

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