+## At least one of the path to the native executable should be defined!\r
+ \r
+## Application supported presets, absolute or relative to \r
+## the JABAWS web application path to the file. Optional.\r
+# <execname>.presets.file=conf/settings/ClustalPresets.xml\r
+\r
+## Application supported parameters, absolute or relative to \r
+## the JABAWS web application path to the file. Optional. \r
+# <execname>.parameters.file=conf/settings/ClustalParameters.xml\r
+\r
+## Application limits, absolute or relative to \r
+## the JABAWS web application path to the file. Optional.\r
+## Use this if you want to limit the size of the job to be accepted by a \r
+## Webservice. The limits files we use in Dundee are provided with JABAWS. \r
+# <execname>.limits.file=conf/settings/ClustalLimits.xml\r
+\r
+## Flags passed to the cluster batch manager for the application. Optional.\r
+## This example sets a maximum execution time to 24 hours and maximum amount of \r
+## memory per task to 6Gb for SGE and OGE cluster batch managers.\r
+## Please note that all the examples of this parameter below are correct for \r
+## Sun Grid Engine or Open Grid Engine (untested) only! If you use a different \r
+## batch manager you would need to specify different flags. \r
+# <execname>.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+## Environmental variables required by native executables. Optional. \r
+## Format: VARIABLE_NAME1#VARIABLE_VALUE1;VARIABLE_NAME2#VARIABLE_VALUE2; \r
+#<execname>.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
+\r
+# Where <execname> is one of [clustalw, mafft, muscle, propcons, tcoffee,\r
+# iupred, jronn, globplot, disembl, aacon]\r
+\r
+\r
+### Parameters specific to the JAVA Jar executables. ### \r
+\r
+## Parameter supported by the executable Jar files, such as jronn and aacon, \r
+## point to the location of the jar file. Also, local.<execname>.bin, \r
+## local.<execname>.bin.windows properties are optional for these, if not \r
+## provided they will be replaced to the java executable path from JAVA_HOME \r
+## environmental variable. \r
+#<execname>.jar.file=binaries/windows/jronn3.1.jar\r
+\r
+ \r