STACEY analyses

[chris blair]

Hi all,

I am playing around with the STACEY tutorial and have a couple questions. The analysis appeared to finish ok, but I kept getting warning messages about version issues. I am using BEAST 2.3.2.

Second, how do you analyze the results with SpeciesDelimitationAnalyser? I keep getting the following error:

Exception in thread "main" java.lang.UnsupportedClassVersionError: dr/app/tools/SpeciesDelimitationAnalyser : Unsupported major.minor version 51.0

at java.lang.ClassLoader.defineClass1(Native Method)

at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)

at java.lang.ClassLoader.defineClass(ClassLoader.java:621)

at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)

at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)

at java.net.URLClassLoader.access$000(URLClassLoader.java:58)

at java.net.URLClassLoader$1.run(URLClassLoader.java:197)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:190)

at java.lang.ClassLoader.loadClass(ClassLoader.java:306)

at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)

at java.lang.ClassLoader.loadClass(ClassLoader.java:247)

P410CBlairs-Bio-iMac:BEAST 2.3.2 Faculty$ 

Lastly I just want to state that this is likely to be a great package that will find widespread use. Will there be the option to include fossil calibrations in the near future? Congrats on the great work Graham.

Chris

[Graham]

Chris,

This is a java version problem. You need Java 8, and you need to make sure your computer uses it. There was a recent discussion here about it, but this old one came up when I searched.
https://groups.google.com/forum/#!topic/beast-users/tjXNXP_kmF0

I haven't thought much about calibrations. I have some other ideas...

Graham Jones

[Graham]

Here's the more recent discussion.
https://groups.google.com/forum/?fromgroups#!topic/beast-users/rJdnQo6EHA0

On Friday, 26 February 2016 20:54:56 UTC, chris blair wrote:

[chris blair]

Thanks Graham it works now. I just want to make sure that STACEY is good to run with BEAST 2.3.2. I still get warnings saying that it wants BEAST 2.4.

Chris

[Graham]

I don't know what is going on there. You should have STACEY 1.1.1 with BEAST 2.3. I have released STACEY 1.2.0 in anticipation of BEAST 2.4, but you should only be able to get that via Beauti 2.4, or if you downloaded it manually from my web site (despite a warning).

Graham

[Christopher Blair]

Yes I am using STACEY 1.1.1. So I was able to go through your tutorial and example file and run my own data file. Regarding the interpretation of the output from SpeciesDelimitationAnalyses, is it best to look at the row with the highest 'count' value? Most of my 'fractions' are very small (e.g. 1.1. e-4) and it appears that the largest is about 0.012. Note that the analysis used only 1 mitochondrial and 1 nuclear locus, with very little variability in the nuclear gene.

Chris

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Christopher Blair, Ph.D.
Assistant Professor

Department of Biological Sciences-New York City College of Technology

Ecology, Evolution and Behavior Program-CUNY Graduate Center

The City University of New York

300 Jay Street

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CBl...@citytech.cuny.edu

Website: https://sites.google.com/site/christopherblairphd/home

[Graham]

If there is little signal in the data, it is typical to get a huge number of possible delimitations with small posterior probabilities, and it's not easy to summarise the result. The delimitation with the highest posterior probability is one thing to look at. You could also consider a similarity matrix like in the DISSECT paper.

Graham