MC3 option in BEAST 1.8.x

[Jacob Berv]

Hi all,

Is there an MCMCMC option in BEAST 1.8.x? I seem to recall there being an option for this in earlier versions. Does anyone know how I can modify the XML to try it? I'm having some convergence issues with a dataset I'm working with and I think it may help.

Best,

Jake

[Santiago Sánchez]

Hi Jacob,

As far as I understand no XML modification is needed to run BEAST's MC3 implementation. All you need is to run it command line using the bin executable beastMC3 or directly using java:

java -Xms64m -Xmx1024m -cp beast.jar dr.app.beast.BeastMC3

If you type the -help flag you will get usage instructions with some examples:

Usage: beastmc3 [-chains <i>] [-delta <r>] [-temperatures] [-swap <i>] [-verbose] [-strict] [-window] [-working] [-overwrite] [-options] [-help]  [-chains <chain-count>] [-delta <temperature-delta>|-temperatures <temperature-list>] [-swap <swap-every>] [-verbose] [-window] [-working] [-help] [<input-file-name>]

    -chains number of chains

    -delta temperature increment parameter

    -temperatures a comma-separated list of the hot chain temperatures

    -swap frequency at which chains temperatures will be swapped

    -verbose verbose XML parsing messages

    -strict Fail on non conforming BEAST XML file

    -window provide a console window

    -working change working directory to input file's directory

    -overwrite Allow overwriting of log files

    -options Display an options dialog

    -help option to print this message

  Example: beastmc3 -chains 3 -delta 1.0 -swap 100 test.xml

  Example: beastmc3 -temperatures 0.2,0.4 -swap 200 -window test.xml

Cheers,

Santiago

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Santiago Sánchez-Ramírez

Department of Ecology and Evolutionary Biology, University of Toronto

Department of Natural History (Mycology), Royal Ontario Museum

100 Queen's Park

Toronto, ON

M5S 2C6

Canada

Other email: santiago...@mail.utoronto.ca

Tel. 416-586-8025

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

[Andrew Rambaut]

As of BEAST 1.8.0 then MCMCMC functionality is in the normal main. Run with:

java -jar beast.jar (or use the shell script in bin/). 

The commandline options are:

    -mc3_chains number of chains
    -mc3_delta temperature increment parameter
    -mc3_temperatures a comma-separated list of the hot chain temperatures
    -mc3_swap frequency at which chains temperatures will be swapped

Best,

Andrew

Andrew Rambaut 

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

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

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

[Jacob Berv]

Cool-What are the default values for these parameters? Is there some place that explains them in more detail?

Jake

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[jithinj...@gmail.com]

Hello,

I had a follow up question on this. Can I run MC3 in BEAST 1.8.4 in CIPRES using the .xml file generate in Beauti 1.8.4 ? If yes, what edits should I make to the .xml files ?

Thanks in advance

Jithin Johnson