BEAST 2

[chris blair]

Hi all, 

I am trying to use either BEAST 1.8 or 2.0.2 and am running into some really strange issues. If I try to run anything via terminal it says the version is 1.6.1. If I double click BEAUti for Mac I get an error that says the file is damaged and should be removed. Any thoughts? Thanks.

Chris

[chris blair]

I figured it out. I had to type the full path to the executable.

[Santiago Sanchez]

Hi Chris,

This is what I usually do when a new version comes up.

Go to..   .../BEAST_v1.8.0/bin

Then..    sudo cp * /usr/bin

Go to..   .../BEAST_v1.8.0/lib

Then..    sudo cp * /usr/lib

Now you should be able to run BEAST (or any program from the suite like TreeAnnotator) from any window in the terminal, just by typing (with no path).

beast ...

Or

treeannotator ...

Etc...

Hope it helps,

Santiago

Santiago Sanchez-Ramirez

Ecology and Evolutionary Biology, University of Toronto

Natural History (Mycology), Royal Ontario Museum

100 Queen's Park

Toronto, ON

M5S 2C6

Canada

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[Andrew Rambaut]

Dear Chris,

I assume you must have v1.6.1 on you command line path. Try typing:

which beast

This should show you where this old version of BEAST resides. It is likely it will be in /usr/local/bin which is the normal

Unix (and Mac) place for command line programs.

If you want to have the new version of beast installed on the command line, I suggest you use symbolic links to the actual

executables.

I assuming the full path of the BEAST package is /Users/myusername/Applications (which might be as good a place as any), type:

cd /usr/local/bin

ln -s ~/Applications/BEAST\ v1.8/bin/beast

(if there is already a beast file there, you will need to delete it first).

Andrew

[Andrew Rambaut]

If you get this error, you may need to go into System Preferences -> Security & Privacy and switch "Allow applications downloaded from anywhere".

Then download the package, and run the programs. You can then turn this option off again if you wish.

Andrew

On 18 Oct 2013, at 21:01, chris blair <blai...@gmail.com> wrote:

[Christopher Blair]

Thanks guys. While I'm here, one more question. Awhile back Santiago suggesting modifying the starting tree in a *BEAST analysis using coalescentSimulator to place the starting species tree within the bounds of the temporal calibrations. Has this issue been fixed with 1.8 so we do not need to manually change the starting tree block in the xml? Thanks.

Chris

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Christopher Blair, Ph.D.
Postdoctoral Associate
Department of Biology
Duke University, Box 90338
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[chris blair]

Apparently not. Andrew and/or Joseph, do you have any recommendations here? Essentially this issue arises when using lognormal calibrations. Right now I am trying to calibrate two nodes, but even if I calibrate one of the nodes I still receive the -INF error. There must be an easier fix to this than completely changing the starting species tree block in the xml whenever I want to use lognormal calibrations for a species tree analysis, no? Thanks guys.

Chris

On Friday, 18 October 2013 16:01:24 UTC-4, chris blair wrote:

[Andrew Rambaut]

This is probably one for Joseph as I don't use *BEAST in my day job. One possibility is to start with normal distributions with small variances and means close to the middle of your desired translated lognormal distributions. Run BEAST for a while and then take the last tree to use as a starting tree.

A.

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___________________________________________________________________
 Andrew Rambaut                
 Institute of Evolutionary Biology       University of Edinburgh
 Ashworth Laboratories                         Edinburgh EH9 3JT
 EMAIL - a.ra...@ed.ac.uk                TEL - +44 131 6508624  

[pepster]

BEAUTI2 should have generated a valid starting file. If not, please send me the XML. If the XML was modified by hand,  contact me and I will try and help.

-Joseph

[Luka Jovanovic]

Hello, I want to plot results from BDSY analysis from BEAST 2. Does anyone know how to calibrate the R code from the tutorial: https://taming-the-beast.org/tutorials/Skyline-plots/ ??

My alignment consists of 9 seq. collected in the 20002-2014 time period. Pls, help this beginner. 
Best regards

Luka Jovanovic, MD, Ph.D candidate

[bitok sot]

Anybody with links to useful materials pertaining to this question? The manual currently available only explains how to generate BDSKY plots for sequences that were collected at single time-point, i.e it only explains how to plot results from BDSKY contemporary, and there is no manual on how to plot results from BDSKY serial analysis. 

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[Luka Jovanovic]

Great point!

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[Luka Jovanovic]

Hello guys,

generally, the code works somehow but the time grid is off. I will attach my log file and graphs that I obtained from the R. You will see that the time frame in the smooth BDSY diagram is so long, and this is the main issue. Please help. Here is the link too: https://taming-the-beast.org/tutorials/Skyline-plots/

Best regards

Luka Jovanovic MD Ph.D. candidate  

 

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