Create a Neighbor-joining phylogenetic tree, with Kimura distance corrections, from a sequence alignment using the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2).
Submit a ClustalW analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#runclustalw2_params_content)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSClustalW2.wsdl
runClustalW2
nj
1
1
nj
1
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
sequence
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#poll_jobid_type)
tooloutput
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSClustalW2.wsdl
poll
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#poll_jobid_type)
toolph
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSClustalW2.wsdl
poll
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#poll_jobid_type)
toolnj
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSClustalW2.wsdl
poll
Wait for job to finish.
Check status of job.
Map job status into true/false is done flag
if(job_status.equals("DONE")) {
is_done = "true";
} else {
is_done = "false";
}
job_status
is_done
If job not finished fail.
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
Get the status of a submited job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#checkstatus_jobid)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSClustalW2.wsdl
checkStatus
EBI job identifier for the job to check.
Status of the job.
A sequence alignment in an appropriate format (e.g. fasta, clustalw or MSF).
User's e-mail address.
EBI job identifier.
Output from the ClustalW program. Useful for diagnosing problems.
The phylogenetic tree in PHYLIP format, for use with tree drawing tools.
Description of the tree.
Completed
EBI_ClustalW2_poll_job
Get_output
Scheduled
Running
Completed
EBI_ClustalW2_poll_job
Get_phylip_tree_result
Scheduled
Running
Completed
EBI_ClustalW2_poll_job
Get_nj_tree_result
Scheduled
Running