TreeAnnotator from command line

[mixam85]

Hi,

How is t possible to use the 'Maximum clade credibility' function of
TreeAnnotator from the command line ( without using the gui ) ?
the -help :
Usage: treeannotator [-heights <keep|median|mean>] [-burnin <i>] [-
limit <r>] [-target <target_file_name>] [-help] <input-file-name>
[<output-file-name>]
-heights an option of 'keep' (default), 'median' or 'mean'
-burnin the number of states to be considered as 'burn-in'
-limit the minimum posterior probability for a node to be annoated
-target specifies a user target tree to be annotated
-help option to print this message

Example: treeannotator test.trees out.txt
Example: treeannotator -burnin 100 -heights mean test.trees out.txt
Example: treeannotator -burnin 100 -target map.tree test.trees
out.txt

Specifies how to use our own target tree but not the 'Maximum clade
credibility'.

Thanks.

[Jamie Oaks]

Hi,

If you don't specify a target tree, treeannotator will default to the
MCC tree, as in the examples in help message. Hope this helps,

Jamie

[harish epuri]

Hi Jamie,

I have one doubt, how to give "Maximum clade credibility, Maximum sum of clade credibility" in command line 

thanks

harish

[Santiago Sanchez]

Hi Harish,

First you need the bin executables in your system path. So if you have a Unix based machine it would be in the /usr/bin folder. You would also need to copy the core beast programs (they are in the lib folder) to /usr/lib . Once you have this set up you can call any BEAST program from any command line shell as:

beauti (will open a java GUI)

beast -beagle your.xml

loganalyser your.log

logcombiner -burnin 50000 your.run1.log your.run2.log your.comb.log

treeannotator -burnin 100 -heights mean your.trees your.mcc.tre

Cheers,

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

+1 416 586 8025

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

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[Miller, Mark]

Just to add a little more from my recent experience, the instructions below will work as long as the default settings in the shell script are fine.

But in my case, I needed more memory. I found you can also call the program directly,

 

> The command line argument I used is java -Xms296m -Xmx16384m -Djava.library.path="/opt/beast/1.8.1/lib"-cp "/opt/beast/1.8.1/lib/beast.jar" dr.app.tools.TreeAnnotator –burnin 3000 -heights mean test2.trees.txt test2.MCC.tree

> java -Xms296m (this sets the startup jvm space)  -Xmx16384m (this sets the maximum heap space to 16GB)

 

Just replace the path to beast.jar in my implementation “/opt/beast/1.8.1/lib” with the correct path in yours.

 

Mark