JABAWS2 client August 2011 http://www.compbio.dundee.ac.uk/jabaws 
 
Usage: <Class or Jar file name> -h=host_and_context <-s=serviceName> ACTION [OPTIONS] 

-h=<host_context>  - a full URL to the JABAWS web server including context 
                     path e.g. http://10.31.1.159:8080/ws
-s=<ServiceName>   - one of [MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, 
					 ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS]
                     <serviceName> is required for all ACTIONS but -list_services

ACTIONS: 
-list_services    - list available services
-test             - test service 
-i=<inputFile>    - full path to fasta formatted sequence file, from which to align 
                    sequences
-parameters       - lists parameters supported by web service
-presets          - lists presets supported by web service
-limits           - lists web services limits

Please note that if input file is specified other actions are ignored

OPTIONS (only for use with -i action):
-r=<presetName>   - name of the preset to use
-o=<outputFile>   - full path to the file where to write an alignment
-f=<PrmInputFile> - the name of the file with the list of parameters to use.

Please note that -r and -f options cannot be used together. Alignment is done with 
either preset or a parameters from the file, but not both!

EXAMPLES: 

1) List all available services on the host 

Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -list_services

2) Test Clustal web service 

Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=ClustalWS -test 

3) Align sequence from file input.txt with Probcons. Record resulting alignment 
into the output.txt 

Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=ProbconsWS -i=input.txt -o=output.txt

4) Calculate disorder with Disembl take input from input.txt, output results to 
the console 

Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=DisemblWS -i=input.txt 

5) List all parameters available for AAconWS service 

Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -parameters

6) Calculate conservation with AAConWS using LANDGRAF method, for Clustal alignment 
from input.txt and report  the scores to the console 

Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -i=input.txt -f=prm.txt 

Where the content of prm.txt file is -m=LANDGRAF
The list of the supported parameters can be obtained as shown in the example 5. 

Citation: Peter V. Troshin, James B. Procter and Geoffrey J. Barton - "Java 
Bioinformatics Analysis Web Services for Multiple Sequence Alignment - 
JABAWS:MSA" Bioinformatics 2011; doi: 10.1093/bioinformatics/btr304.