BEAST v1.8.3 released

[Andrew Rambaut]

Dear BEAST Users,

We have just posted a small update to BEAST 1 - v1.8.3

Available in binaries for Mac, Windows and Linux (.dmg, .zip, .tgz). The Linux version
can also be installed on Macs as a command line version:

https://github.com/beast-dev/beast-mcmc/releases/tag/v1.8.3

New Features in this verison:
Generalized Stepping Stone sampling for Marginal Likelihood Estimation.
Continuous quantile version of uncorrelated relaxed clock as option in
BEAUti [from Li & Drummond 2012, MBE].
Option in BEAUti to log complete histories in Markov Jump Counting.
Jukes-Cantor added as an option for BEAUti nucleotide substition model.
New tree transition kernel (SubTreeLeap operator) implementd in BEAST.
Defaulting to randomizing rate categories for DiscretizedBranchRates.
BEAUti 'guess dates' options are now persistent from run to run (and
shared with Path-O-Gen/Tempest).
Transmission tree model of Hall et al (2016) implemented.
Fast, general multidimensional scaling (MDS) implemented.
Clock panel in BEAUti simplified.
Parameter linking available in Priors panel in BEAUti.
Command line is logged into log file headers for reference.

Plus bug fixes.

[Santiago Sánchez]

Dear Andrew,

I'm testing v1.8.3 on a Linux machine running Ubuntu and in the clock panel in BEAUti there is no box to enter a fixed subst./mutation rate. Just wanted to report it in case this is a bug.

Cheers,

Santiago

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Santiago Sánchez-Ramírez

Environmental Genomics Group

Max Planck Institute for Evolutionary Biology

August-Thienemann-Str. 2
24306 Plön
Germany

Website: https://sites.google.com/site/santiagosnchezrmirez/

[Santiago Sánchez]

I'm also getting this error when running *BEAST on the example xml: birthDeathMultiLoci.xml, and on my own data.

dr.xml.XMLParseException: The '<gammaDistributionModel>' element with id, 'null', is incorrectly constructed.

The following was expected:

Exactly one ELEMENT of name shape REQUIRED containing

    Exactly one ELEMENT of type Parameter REQUIRED

at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.parse(Unknown Source)

at dr.app.beast.BeastMain.<init>(Unknown Source)

at dr.app.beast.BeastMain.main(Unknown Source)

Feb 15, 2016 12:04:28 PM dr.app.beast.BeastMain <init>

SEVERE: Parsing error - poorly formed BEAST file, birthDeathMultiLoci.xml:

The '<gammaDistributionModel>' element with id, 'null', is incorrectly constructed.

The following was expected:

Exactly one ELEMENT of name shape REQUIRED containing

    Exactly one ELEMENT of type Parameter REQUIRED

java.lang.RuntimeException: Terminate

at dr.app.beast.BeastMain.<init>(Unknown Source)

at dr.app.beast.BeastMain.main(Unknown Source)

I checked the XML and it looks fine.

[Andrew Rambaut]

Dear Santiago,

I will look into this - I simplified the clock UI. My intention for fixing any parameter

is simply to set the initial value and then turn on off the operators - is that not possible?

Andrew

[Andrew Rambaut]

Hi Santiago,

Thanks for pointing this out. I don’t have anything to do with *BEAST so I didn’t test it (but I also didn’t expect

the changes I made to effect it - I was wrong). Anyway, I think I have fixed this issue (birthDeathMultiLoci.xml runs

now). Rather than releasing a new version, I have just updated the binaries in the v1.8.3 release so please download

again and try. 

Andrew

[Lin Marco]

Dear Andrew,

I have a question about the option of continuous quantile parameterization for uncorrelated relaxed clock.

I try to understand the references( Model Averaging and Bayes Factor Calculation of Relaxed

Molecular Clocks in Bayesian Phylogenetics. Li & Drummond 2012, MBE), but It does not let me know who the situation should be checked or not.

Could you please description what difference between checked or not checked that option?

Thank you very much

Regards,

Marco

rambaut於 2016年2月13日星期六 UTC+8下午11時18分14秒寫道：