BEAST v1.8.2 released

[Andrew Rambaut]

Dear BEAST-Users,

BEAST v1.8.2 has been released and is available for download. 

Details and download links are on the BEAST website:

http://beast.bio.ed.ac.uk/downloads

Source code is available on GoogleCode:

http://beast-mcmc.googlecode.com

This release fixes some bugs including the one where the BEAST process was closing once the run was over (on UNIX machines).

This is a development of the BEAST v1.x software and is independent of BEAST2 which is available on http://beast2.org/

Here is the updated history:

2015-03-05 - v1.8.2

Bugs fixed:

• Issue 747: Robust counting with multiple partitions generates unique reference IDs in BEAUti and unique total counts for Tracer.

• Issue 756: FEE with random local clock + codon position partitions + multiple threads.

• Issue 754: BEAST v1.8.1 is not terminating leaving 'zombie' processes

• Issue 749: Multiple partitions with unlinked substitution models can turn on ancestral state reconstruction.

• Issue 747: Duplicate references in robust counting with multiple partitions.

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

 

Andrew Rambaut 

Institute for Evolutionary Biology | Centre for Infection, Immunity & Evolution 

Ashworth Laboratories, University of Edinburgh, Edinburgh, EH3 9JT, UK

contact – a.ra...@ed.ac.uk | http://tree.bio.ed.ac.uk | tel +44 131 6508624

[David Cannatella]

Andrew et al.,

There seems to be a problem with this version of BEAUTI, using either Java JRE 7 or 8.

I'm running Yosemite 10.10.2. Here's what I did.

I imported the primates.nex dataset. I selected both partitions and then clicked "Link Clock Models".

Create New Partition Clock Model window appears. But, there are text fields or other user interface widgets (see screen grab below). The same applies for Link Substitution models.

Similarly, when I define a taxon group and try to make it monophyletic, there is no check box with which to select "Monophyly", or "Stem" for that matter.

I verified that BEAUTI 1.7.5 works fine under either Java 7 or 8.

Dave

David Cannatella 

Department of Integrative Biology

Associate Chair of Biodiversity Collections

Patterson Labs, 2415 Speedway

University of Texas            

Austin, Texas 78712

www.cannatellalab.org

512-453-1620 (cell; voicemail)

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[Andrew Rambaut]

There does seem to be issues with the UI on Mac Yosemite. It seems to be an issue with Java 7/8 and is specific to Mac. I will fix it shortly.

The solution for the moment is to double click ‘beauti.jar’ in the lib folder. This works fine.

Andrew

On 5 Mar 2015, at 18:58, David Cannatella <davidca...@gmail.com> wrote:

Andrew et al.,

There seems to be a problem with this version of BEAUTI, using either Java JRE 7 or 8.

I'm running Yosemite 10.10.2. Here's what I did.

I imported the primates.nex dataset. I selected both partitions and then clicked "Link Clock Models".

Create New Partition Clock Model window appears. But, there are text fields or other user interface widgets (see screen grab below). The same applies for Link Substitution models.

Similarly, when I define a taxon group and try to make it monophyletic, there is no check box with which to select "Monophyly", or "Stem" for that matter.

I verified that BEAUTI 1.7.5 works fine under either Java 7 or 8.

Dave

<BEAST_Problem.tiff>

[Andrew Rambaut]

This issue is now fixed. Anyone that downloaded the Mac version of v1.8.2 should re-download load it now. It is only the Mac version that had this issue and is now updated.

Thanks, David, for pointing it out.

Andrew

On 5 Mar 2015, at 18:58, David Cannatella <davidca...@gmail.com> wrote:

Andrew et al.,

There seems to be a problem with this version of BEAUTI, using either Java JRE 7 or 8.

I'm running Yosemite 10.10.2. Here's what I did.

I imported the primates.nex dataset. I selected both partitions and then clicked "Link Clock Models".

Create New Partition Clock Model window appears. But, there are text fields or other user interface widgets (see screen grab below). The same applies for Link Substitution models.

Similarly, when I define a taxon group and try to make it monophyletic, there is no check box with which to select "Monophyly", or "Stem" for that matter.

I verified that BEAUTI 1.7.5 works fine under either Java 7 or 8.

Dave

<BEAST_Problem.tiff>

Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3FL, UK

[lingo]

On 2015-03-10 at noon, there was no version 1.8.2 at the download site, at least und Windows 7. What is going on?

[Andrew Rambaut]

The link in the beast.bio.ed.ac.uk leads you here: http://tree.bio.ed.ac.uk/software/beast/ which is where the downloads are.

Have updated the version number on the first page now.

Andrew

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Andrew Rambaut 

Institute for Evolutionary Biology | Centre for Infection, Immunity & Evolution 

Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3FL, UK