Given a set of sequences perform an multiple sequence alignment and from the multiple alignment derive a phylogenetic tree. The popular ClustalW program (see http://www.clustal.org/), as implemented in the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2) is used to perform both tasks.
Align the sequences.
Perform a ClustalW multiple sequence alignment using the EBI’s WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2). The set of sequences to align are the input, the other parameters for the search (see Job_params) are allowed to default.
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
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#poll_jobid_type)
toolaln
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSClustalW2.wsdl
poll
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
1
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)
tooldnd
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)
tooloutput
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSClustalW2.wsdl
poll
Check for job status, and wait if job not finished.
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.
Sequences to align (fasta format recommended).
User e-mail address.
The alignment in ClustalW format.
Guide tree used to produce the final alignment.
text/xml
EBI job identifier
Completed
EBI_ClustalW2_poll_job
Get_alignment_result
Scheduled
Running
Completed
EBI_ClustalW2_poll_job
Get_guide_tree_result
Scheduled
Running
Completed
EBI_ClustalW2_poll_job
Get_output_result
Scheduled
Running
Create a phylogenetic tree from the alignment.
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
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)
toolph
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSClustalW2.wsdl
poll
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
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
nj
1
1
nj
1
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)
toolnj
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
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
Input set of sequences to be aligned.
User e-mail address.
Multiple sequence alignment in ClustalW format.
Neighbour-joining phylogenetic tree in PHYLIP format.