JABAWS MANUAL
@@ -86,20 +88,14 @@ Please note that -r and -f options cannot be used together. Alignment is done wi --fastaparttree--retree=10
--op=2.2 -
The format of the file is the same for all JABAWS web services. Parameters are specified in exactly the same way as for native executables - alignment programs like Mafft etc. So parameters which you can use with command line version of an alignment program can be used with JABAWS. Most of the settings controlling alignment process are supported, but the setting controlling output are not. This is due to the fact the output have to be handled by JABAWS, so must remain within its control. For a list of parameters supported by a web service see the next example. In prm.in parameters are separated by the new line, and name of the parameter is separated from its value with an equal sign. This format is constant no matter which JABAWS web service is used.
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The format of the file is the same for all JABAWS web services. Parameters are specified in exactly the same way as for native executables - alignment programs like Mafft etc. So parameters which you can use with command line version of an alignment program can be used with JABAWS. Most of the settings controlling alignment process are supported, but because any output has to be handled by JABAWS, settings controlling output are not allowed to be changed. For a list of parameters supported by a web service see the next example. In prm.in parameters are separated by the new line, and name of the parameter is separated from its value with an equals sign. This format is constant no matter which JABAWS web service is used.
java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -parameters
The same client can be used to access JABAWS on different hosts. Just point the client to the host you want to use by changing the value of -h key. For example you used -h=http://myhost.compbio.ac.uk:8080/jabaws server, now you want to use another server to -h=http://mylabserver.myuni.edu. This comes handy if your favorite server is off and you need to do the job yesterday.
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