TreeLogAnalyser

From BEAST Software

This program assists in summarizing the clades information from a sample of trees produced by BEAST and named as *.trees file.

Contents 1 Program Arguments 2 Running TreeLogAnalyser 2.1 Windows 2.2 Mac / Linux / Unix

Program Arguments

- burnin                    "the number of states to be considered as 'burn-in' [default = none]";
- export file-name          "name of file to export";
- limit                     "don't export trees with support lower than limit [default = 0.0]";
- probability               "credible set probability limit [default = 0.95]";
- max                       "export no more than max trees [default = all]";
- short                     "use this option to produce a short report";
- help                      "option to print this message".

Running TreeLogAnalyser

1) Simple command to run TreeLogAnalyser from beast.jar which is available in the /lib folder of released BEAST package

java -cp beast.jar dr.app.tools.TreeLogAnalyser inputTrees.trees

2) Or create a script file in the /bin folder of released BEAST package

Windows

treeloganalyser.cmd

@echo off
setlocal
if ""=="%BEAST%" set BEAST=%~dp0%..
set BEAST_LIB=%BEAST%\lib
java -Xms64m -Xmx1024m -Djava.library.path="%BEAST_LIB%" -cp "%BEAST_LIB%/beast.jar" dr.app.tools.LogAnalyser %*

Mac / Linux / Unix

treeloganalyser.sh

#!/bin/sh

if [ -z "$BEAST" ]; then
	## resolve links - $0 may be a link to application
	PRG="$0"

	# need this for relative symlinks
	while [ -h "$PRG" ] ; do
	    ls=`ls -ld "$PRG"`
	    link=`expr "$ls" : '.*-> \(.*\)$'`
	    if expr "$link" : '/.*' > /dev/null; then
		PRG="$link"
	    else
		PRG="`dirname "$PRG"`/$link"
	    fi
	done

	# make it fully qualified
	saveddir=`pwd`
	BEAST0=`dirname "$PRG"`/..
	BEAST=`cd "$BEAST0" && pwd`
	cd "$saveddir"
fi

BEAST_LIB="$BEAST/lib"
java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.TreeLogAnalyser $*