MSA_PAD_Gene_Mode__DFile_name00 Test_file 2014-08-07 10:56:38.292 UTC Filename of your choice for the input file 2014-08-07 10:56:31.171 UTC InputBody00 >ABY27676/1-453 ABY27676 TTAATATTAGGAGCTCCAGATATAGCTTTTCCTCGAATAAATAATCTTAGTTTTTGGTTGCTTCCTCCTTCTTTGATTTTATTA ATAATTTCTTCAATAGTGGAGATAGGGGTTGGGGCGGGGTGAACTATTTATCCTCCTTTATCGGGTAGTCTA GGTCATTCAGGGGTTTCAGTAGATTTAGCTATTTTTAGCTTACATTTGGCGGGAGCTTCTTCAATTATAGGA GCAATTAATTTTATTTCCACTATTTTAAATATACGTTCAGTTGGGATATCTATAGATAAGGTACCTTTATTT GTGTGATCTGTATTAGTTACTGCTGTTTTATTATTATTATCTTTACCAGTTTTAGCCTGGGGTATTACGATA TTATTAACAGATCGAAATTTTAACACTTCTTTTTTTGACCCTGCGGGTGGAGGTGATCCAATTTTATTTCAA CATCTTTTT >ADW61587/1-657 ADW61587 ACGTTATATTTAATATTTGGGGCTTGAGCTGCTATAGTAGGAACAGCCATAAGAGTATTAATTCGAATTGAA TTAGGTCAACCTGGGAGGTTTATTGGGGATGATCAATTATATAATGTAATCGTTACTGCTCATGCATTTGTT ATAATTTTTTTTATAGTAATACCTATTTTGATTGGAGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGC GCTCCTGATATAGCTTTTCCTCGTATAAATAATTTAAGATTTTGGCTACTCCCTCCTTCATTATTTTTATTA ATTATTTCTTCTATAGTAGAAATGGGAGTGGGGGCAGGATGGACGGTTTATCCTCCTTTAGCTAGTTTAGAG GGCCATGCTGGCAGGTCAGTGGATTTTGCTATTTTTTCTTTACATTTAGCGGGGGCCTCCTCTATTATGGGG GCTATTAATTTTATTTCTACTATTATTAATATACGATCGCATGGAATAACTATAGAAAAAGTACCTTTATTT GTATGATCAGTATTGATTACTGCTGTATTATTATTATTATCACTTCCAGTATTGGCGGGGGCTATCACAATA TTATTAACTGATCGAAATTTTAATACTTCGTTTTTTGACCCTTCAGGAGGGGGGGATCCAATCCTTTTCCAA CATTTATTT >AEE92862/1-657 AEE92862 ACGTTATATTTTGTTTTTGGAGCTTGATCTGCTATGGTAGGGACCGGAATAAGAGTAATTATTCGGTCTGAG TTGGGGCAAGTGGGGAGATTGTTGGGTGATGATCATATATATAATGTTATGGTAACTGCTCATGCTTTAGTA ATGATTTTTTTTATGGTAATGCCAATCATGATTGGAGGTTTTGGTAATTGATTACTGCCTTTAATAGTAGGA GCTCCTGATATGGCTTTTCCTCGTATAAATAATTTGAGTTTTTGATTGCTTCCACCTTCTTTATTTTTGTTG GTGTTGTCTTCTTTAACAGATGTTGGGGTAGGGGCTGGTTGAACTATTTATCCTCCTTTGTCTTCGGGAGTT GGGCATGGAGGTGGGGGTATGGATTTTGCTATTTTTTCTTTGCATTTAGCTGGGGCTTCTTCTATTATGGGG GCGATTAATTTTATTACCACTATTATTAATATGCGTACAAATGGTATAACTATGGAGCGTGTGCCGTTGTTT GTGTGATCAGTATTAGTGACTGCTATTTTGTTATTATTGTCTTTACCAGTATTGGCGGGGGCTATTACGATA TTACTAACAGATCGTAATTTTAATACATCTTTTTTTGATCCTGCTGGAGGAGGGGATCCTGTTCTGTTTCAG CATTTATTT >AEC60810/1-657 AEC60810 ACTTTGTATTTATTGTTTGGTATTTGATCTGCTATAATGGGAACGGCAATAAGAGTGATTATTCGAATTGAA TTAGGTCAAGTTGGAAGATTGTTGGGTGATGATCATTTATATAATGTAATTGTAACAGCACATGCTTTGGTT ATGATTTTTTTTATAGTTATACCGATTTTGATTGGTGGATTTGGAAATTGAATAGTTCCTTTGATGTTAGGT GCTCCAGATATAGCATTCCCACGTATAAATAATTTGAGATTTTGATTGCTTCCTCCATCATTATTTTTGTTA TTATTATCTTCTTTAACAGATGTAGGGGTTGGAGCCGGGTGAACTATTTATCCTCCTTTATCCTCTGGGGTT GGACATAGAGGGGGGGGGATGGATTTTGCTATTTTTTCTTTACATTTAGCAGGAGCTTCATCTATTATAGGG GCGATTAATTTTATTACAACAATTATTAATATGCGAAGATTTGGAATAACAATAGAACGTGTACCTTTATTT GTGTGATCAGTTCTTATTACTACTATTTTATTATTGCTTTCTTTACCTGTATTGGCTGGTGCTATTACTATA TTGTTGACTGATCGAAATTTCAATACTTCTTTTTTTGATCCTGCTGGAGGTGGTGATCCTATTTTGTTTCAA CATTTATTT >AEE92861/1-633 AEE92861 TGATCTGCTATGGTAGGTACCGGAATAAGAGTAATTATTCGGTCTGAG TTGGGGCAAGTGGGAATATTATTAGGTGATGATCATATATATAATGTTATGGTTACTGCTCATGCTTTAGTA ATGATTTTTTTTATGGTAATGCCAATCATGATTGGAGGTTTTGGTAATTGATTATTGCCTTTAATGGTAGGA GCTCCTGATATGGCTTTTCCTCGTATAAATAATTTGAGTTTTTGATTGCTTCCTCCTTCTTTATTTTTGTTG GTGTTGTCTTCTTTAACAGATGTTGGGGTAGGGGCTGGTTGAACTATTTATCCTCCTTTGTCTTCGGGAGTT GGGCATGGAGGTGGGGGTATGGATTTTGCTATTTTTTCTTTGCATTTAGCTGGGGCTTCTTCTATTATGGGG GCGATTAATTTTATTACTACTATTATTAATATGCGTACAAATGGTATGACTATGGAGCGTGTGCCGTTGTTT GTGTGATCAGTATTAGTGACTGCTATTTTGTTATTGTTGTCTTTGCCAGTATTGGCGGGGGCTATTACAATA TTATTGACAGATCGTAATTTTAATACATCTTTTTTTGATCCTGCTGGAGGAGGGGATCCTGTTCTGTTTCAA CATTTATTT >AEE92860/1-648 AEE92860 TTTGTTTTTGGAGCTTGATCTGCTATGGTAGGTACCGGAATAAGAGTAATTATTCGGTCTGAG TTGGGGCAAGTGGGAAGATTATTAGGTGATGATCATATATATAATGTTATGGTTACTGCTCATGCTTTAGTA ATGATTTTTTTTATGGTAATGCCAATCATGATTGGAGGTTTTGGTAATTGATTATTGCCTTTAATGGTAGGA GCTCCTGATATGGCTTTTCCTCGTATAAATAATTTGAGTTTTTGATTGCTTCCTCCTTCTTTATTTTTGTTG GTGTTGTCTTCTTTAACAGATGTTGGGGTAGGGGCTGGTTGAACTATTTATCCTCCTTTGTCTTCGGGAGTT GGGCATGGAGGTGGGGGTATGGATTTTGCTATTTTTTCTTTGCATTTAGCTGGGGCTTCTTCTATTATGGGG GCGATTAATTTTATTACTACTATTATTAATATGCGTACAAATGGTATGACTATGGAGCGTGTGCCGTTGTTT GTGTGATCAGTATTAGTGACTGCTATTTTGTTATTGTTGTCTTTGCCAGTATTGGCGGGGGCTATTACAATA TTATTGACAGATCGTAATTTTAATACATCTTTTTTTGATCCTGCTGGAGGAGGGGATCCTGTTCTGTTTCAA CATTTATTT >ADD09384/1-555 ADD09384 TATCAGCTATACAATGTATTAATTACCGCTCATGCTATAATT ATGGTATTTTTCATGATTATGCCAGCTTTATTTGGTGGATTTGGTAATTACTTTGTACCAATTTTAATAGGT GCCCCGGATATGGCTTTTCCTAGGCTAAATAATATAAGTTTTTGGCTACTTGTCCCTGCTTTTATATTATTA ATGCTGTCAGGTTTGGTTGATGGAGGAGCTGGTACTGGCTGGACACTGTATCCTCCTCTAAGTAGTATAGTA GGGCATCCTGGCGCTGCTGTCGATATGGCTATTTTAAGCTTACATCTTACAGGGCTTTCCTCCATTCTTGGT TCAATTAATATGATTGTCACTATCTTTAATATGAGAACTGATGGTATGGGGTTATTTGAAATGCCCTTATTT GTTTGGTCAATTTTGGTTACTGCCTTCTTGCTGATACTAGCAATTCCTGTGTTAGGGGGTGCAATAACCATG TTACTGACTGATCGAAATTTTGGTACTACTTTTTTCAAGCCTGATGGTGGCGGAGATCCAGTGTTATTTCAG CATTTATTT >ADJ82639/1-645 ADJ82639 ACTTTATATTTAATGTTTGGGGTTTGGTCAGCTATAATAGGAACTGCTATAAGAGTATTAATTCGAATGGAA TTAGGGAATCCTGGTAGATTGTTAGGTGATGATCATTTGTATAATGTTATAGTTACTGCTCATGCTTTTGTA ATAATTTTTTTTATAGTAATGCCTATTCTTATTGGAGGTTTTGGAAATTGATTAGTTCCTTTAATATTAGGA GCTCCAGATATATCATTTCCTCGAATAAATAATCTTTCTTTTTGATTATTACCTCCTTCTTTATTTTTGTTA TCTATATCTTCTATAGTAGAAATAGGAGTTGGGGCTGGGTGAACTGTTTATCCTCCTTTAGCGTCTACAGTT GGGCACATAGGAAATTCAATAGATTTTGCTATTTTTTCTCTTCATTTAGCTGGAGCTTCTTCTATTATAGGA GCTGTAAATTTTATTTCTACCATTATTAATATACGAATATTAGGAATATCTATAGAGAAGGTTCCTCTTTTT GTTTGATCAGTTTTAATTACAGCAGTATTATTATTACTTTCTTTACCTGTTTTAGCAGGTGCTATTACTATA TTATTAACAGATCGAAATTTTAATACTTCTTTTTTTGATCCTGCTGGGGGAGGAGATCCTAATTTATTT >ADQ21240/1-648 ADQ21240 AGATTATATTTTGTTTTTGGGGCTTGAGCTGCTATAGTAGGAACAGCAATAAGAGTATTAATTCGTGTTGAG TTGGGACAAACTGGTAGTTTGTTAGGGGATGATCAGTTGTATAATGTTATTGTTACGGCTCATGCTTTTGTA ATAATTTTTTTTATAGTTATGCCTATTTTAATTGGGGGTTTTGGAAATTGGCTGATTCCACTAATACTAGGA GCTCCGGATATAGCTTTCCCTCGTATAAATAATTTGAGATTTTGGCTTTTACCCCCTTCTTTATTATTACTG TTTATTTCAAGCATAGATGAGATAGGAGTGGGGGCGGGATGAACGGTTTACCCCCCTCTTGCCTCTTTAGAG GGACATTCTGGTAGTTCAGTAGATTTTGCTATTTTTTCTTTACACTTAGCTGGAGCGTCTTCTATTATAGGG GCTATTAATTTTATTTCCACAATTTTGAATATACGGGGTTATGGAATATCTATAGAAAAAGTACCTTTATTT GTTTGGTCCGTGTTAATTACAGCTGTATTATTATTGTTATCTCTTCCTGTGTTAGCTGGGGCTATCACAATA TTACTGACGGATCGTAATTTTAATACTTCATTTTTTGATCCTTGTGGGGGGGGGGATCCTGTTTTGTTTCAA >AEE92882/1-657 AEE92882 ACGTTATATTTTGTTTTTGGAGCTTGATCTGCTATGGTAGGGACCGGAATAAGAGTAATTATTCGGTCTGAG TTGGGGCAAGTGGGGAGATTGTTGGGTGATGATCATATATATAATGTTATTGTAACTGCTCATGCTTTAGTA ATGATTTTTTTTATGGTAATGCCAATCATGATTGGAGGTTTTGGTAATTGATTACTGCCTTTAATAGTAGGA GCTCCTGATATGGCTTTTCCTCGTATAAATAATTTGAGTTTTTGATTGCTTCCACCTTCTTTATTTTTGTTG GTGTTGTCTTCTTTAACAGATGTTGGGGTAGGGGCTGGTTGAACTATTTATCCTCCTTTGTCTTCGGGAGTT GGGCATGGAGGTGGGGGTATGGATTTTGCTATTTTTTCTTTGCATTTAGCTGGGGCTTCTTCTATTATGGGG GCGATTAATTTTATTACCACTATTATTAATATGCGTACAAATGGTATAACTATGGAGCGTGTGCCGTTGTTT GTGTGATCAGTATTAGTGACTGCTATTTTGTTATTATTGTCTTTACCAGTATTGGCGGGGGCTATTACGATA TTACTAACAGATCGTAATTTTAATACATCTTTTTTTGATCCTGCTGGAGGAGGGGATCCTGTTCTGTTTCAG CATTTATTT >ADW58691/1-657 ADW58691 ACTTTATATTTAATATTTGGAGCTTGATCTGCTATAGTAGGGACTGCTATAAGAGTGTTAATTCGAATAGAA TTAGGTCAATCTGGAAGACTTTTAGGTGATGATCATTTATATAATGTTGTAGTTACTGCACATGCTTTTGTT ATAATTTTTTTTATAGTTATACCTATTTTGATTGGTGGTTTTGGAAATTGGTTAGTTCCTTTAATATTAGGT GCTCCTGATATAGCTTTTCCTCGAATAAATAATTTAAGTTTTTGATTATTACCTCCTTCTTTATTTTTATTA TTTATTTCTTCTATAGTTGAAATAGGAGTTGGAGCAGGATGAACAGTTTATCCTCCATTGGCATCTAGTGTA GGTCATATGGGAAGTGCAATAGATTTTGCTATTTTTTCATTACATTTGGCTGGTGCTTCTTCTATTATAGGA GCAGTAAATTTTATTACTACTATTATTAATATACGTTCTCATGGAATAAGAATAGAAAAAGTTCCTTTATTT GTTTGATCAGTTTTAATTACAGCTATTTTGTTGTTATTATCTTTACCTGTTTTAGCAGGTGCTATTACTATA TTATTAACTGATCGTAATTTTAATACTTCTTTTTTTGATCCTGCTGGAGGAGGAGATCCTATTTTATTTCAA CATTTATTT >ADW58631/1-657 ADW58631 ACTTTATATTTAATATTTGGAGCTTGATCTGCTATAGTAGGGACTGCTATAAGAGTGTTAATTCGAATAGAA TTAGGTCAATCTGGAAGACTTTTAGGTGATGATCATTTATATAATGTTGTAGTTACTGCACATGCTTTTGTT ATAATTTTTTTTATAGTTATACCTATTTTGATTGGTGGTTTTGGAAATTGGTTAGTTCCTTTAATATTAGGT GCTCCTGATATAGCTTTTCCTCGAATAAATAATTTAAGTTTTTGATTACTACCTCCTTCTTTATTTTTATTA TTTATTTCTTCTATAGCTGAAATAGGAGTTGGAGCAGGATGAACAGTTTATCCTCCATTGGCATCTAGTGTA GGTCATATAGGAAGTGCAATAGATTTTGCTATTTTTTCATTACATTTGGCTGGTGCTTCTTCTATTATAGGA GCAGTAAATTTTATTACTACTATTATTAATATACGTTCTCATGGAATAAGAATAGAAAAAGTTCCTTTATTT GTTTGATCAGTTTTAATTACAGCTATTTTGTTGTTATTATCTTTACCTGTTTTAGCAGGTGCTATTACTATA TTATTAACTGATCGTAATTTTAATACTTCTTTTTTTGATCCTGCTGGAGGAGGAGATCCTATTTTATTTCAA CATTTATTT >ACM89220/1-657 ACM89220 ACTTTATATTTTTTATTTGGTACTTGATCAGCAATAATTGGTACAGCAATAAGTGTTTTAATTCGTGTTGAA CTAGGATTTTCTGGAAGATTTTTAGGTGATGATCATTTATATAATGTAATTGTTACTGCTCATGCTTTTATT ATAATTTTTTTTATAGTTATACCTATTTTAATTGGTGGTTTTGGAAATTGGTTAGTTCCTTTAATATTAAGA GCTCCAGATATAGCTTTTCCTCGTATAAATAATTTAAGATTTTGGTTACTACCTCCTTCGTTATTATTGTTA TTTATTTCTTCTATGGTTGAAATCGGAGTTGGAGCAGGGTGGACTATTTATCCTCCTTTATCTTCTTCTGTG GGTCATTCTGGTGCATCTATGGATTTTGCAATTTTTTCTCTTCATTTAGCTGGTGCTTCTTCTATTATAGGT GCTATTAATTTTATTTCAACAATTATTAATATACGACCTTATGGTATAAGAATAGAAAAGATTCCTTTATTT GTATGATCTGTATTAATTACAGCTGTCTTATTATTATTATCATTACCAGTATTAGCTGGGGCTATTACTATA CTTTTAACTGATCGTAATTTTAATACTTCTTTTTTTGATCCAGCTGGGGGTGGGGATCCAATTTTATTTCAG CATTTATTT >AEE92867/1-642 AEE92867 TTTGGGGCTTGATCTGCTATGGTAGGTACCGGAATAAGAGTAATTATTCGGTCTGAG TTGGGGCAAGTGGGAAGATTATTAGGTGATGATCATATATATAATGTTATGGTTACTGCTCATGCTTTAGTA ATGATTTTTTTTATGGTAATGCCAATCATGATTGGAGGTTTTGGTAATTGATTATTGCCTTTAATGGTAGGA GCTCCTGATATGGCTTTTCCTCGTATAAATAATTTGAGTTTTTGATTGCTTCCTCCTTCTTTATTTTTGTTG GTGTTGTCTTCTTTAACAGATGTTGGGGTAGGGGCTGGTTGAACTATTTATCCTCCTTTGTCTTCGGGAGTT GGGCATGGAGGTGGGGGTATGGATTTTGCTATTTTTTCTTTGCATTTAGCTGGGGCTTCTTCTATTATGGGG GCGATTAATTTTATTACTACTATTATTAATATGCGTACAAATGGTATGACTATGGAGCGTGTGCCGTTGTTT GTGTGATCAGTATTAGTGACTGCTATTTTGTTATTGTTGTCTTTGCCAGTATTGGCGGGGGCTATTACAATA TTATTGACAGATCGTAATTTTAATACATCTTTTTTTGATCCTGCTGGAGGAGGGGATCCTGTTCTGTTTCAA CATTTATTT >ADH12119/1-645 ADH12119 ACTTTATACTTGGTTTTTGGTGCTTGAGCGGCTATGGTTGGAACTGCAATAAGTGTTTTAATTCGAATTGAG TTGGGGCAATCTGGTAGATTTATGGGAGATGATCAGTTGTATAATGTTATTGTAACTGCTCATGCTTTTGTT ATAATTTTTTTTATGGTTATGCCTATTTTGATTGGGGGCTTTGGTAATTGACTGGTTCCTTTGATGTTGGGG GCTCCTGATATGGCTTTTCCTCGCATGAATAATTTAAGGTTTTGATTATTGCCTCCTTCTTTATTTTTATTA TTTATTTCTTCTATGGTGGAAATAGGGGTTGGGGCTGGTTGAACGATCTACCCTCCTTTAGCGTCTCTAGAA GGACATTCAGGAAGTTCGGTTGATTTTGCCATTTTTTCTTTGCATTTGGCTGGGGCCTCTTCTATTATAGGG GCTATTAATTTTATTTCTACAATTTTGAATATACGGTCTTATGGGATGTCTATGGAAAAAGTTCCTTTGTTT GTTTGGTCGGTTTTAATTACTGCTGTTTTGCTCCTATTATCACTTCCGGTTTTAGCTGGGGCTATCACTATG TTATTAACTGATCGAAATTTTAATACATCGTTTTTTGATCCTTCGGGGGGAGGGGATCCTATTTTTTTT 2014-08-07 10:55:51.692 UTC DNA sequences in FASTA format 2014-08-07 10:54:51.963 UTC Email00 balechbachir@gmail.com 2014-08-07 10:59:55.348 UTC Email where notification of job completion will be sent 2014-07-04 09:08:56.237 UTC GeneticCode00 Insert one of the following genetic code: 1,2,3,4,5,6,9,10,11,12,13,14,15,16,21,22,23,25 2014-08-07 10:58:51.524 UTC 5 2014-08-07 10:58:55.436 UTC Frames00 1,2,3,-1,-2,-3 2014-08-07 10:59:37.780 UTC Insert Frame/s value/s: values must be comma-separated 2014-08-07 10:59:28.228 UTC Log0FileName0 File name to be used in the evalutation phylogenetic inference workflow 2014-07-04 09:11:03.385 UTC JobID0 Use this number as in input in phylogenetic evalutation workflow 2014-07-04 09:09:19.346 UTC JSTWebDav3InputToken0File_name0InputBody0REST_Service_redirection00StatusMKDIR00net.sf.taverna.t2.componentcomponent-activity1.5net.sf.taverna.t2.component.ComponentActivity http://www.myexperiment.org JSTInteraction JSTWebDav3Input 3 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRandGenout00net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity out 0 0 workflow org.embl.ebi.escience.scuflworkers.java.TestSometimesFails UserNameHere 2013-05-27 13:52:26.399 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeNoSpacestring0out100net.sf.taverna.t2.activitiesbeanshell-activity1.5net.sf.taverna.t2.activities.beanshell.BeanshellActivity string 0 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeTargetOnlystring0out100net.sf.taverna.t2.activitiesbeanshell-activity1.5net.sf.taverna.t2.activities.beanshell.BeanshellActivity string 0 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeREST_Servicename0mail0arguments0responseBody00net.sf.taverna.t2.activitiesrest-activity1.5net.sf.taverna.t2.activities.rest.RESTActivity GET http://webgateway.ba.infn.it:8080/INFN.Grid.RestFrontEnd/services/QueryJob/InsertJobs?NAME={name}&arguments={arguments}&mail={mail} application/xml application/xml String false false false false true mail java.lang.String arguments java.lang.String name java.lang.String net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeText_constantvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity MsaPadGene net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXPath_Servicexml_text0firstNode00net.sf.taverna.t2.activitiesxpath-activity1.5net.sf.taverna.t2.activities.xpath.XPathActivity <?xml version="1.0" encoding="UTF-8"?> <Job><Name>blast</Name><Flag>7772590c-d7ab-4b76-98b9-aa293c6c34fe</Flag><JobsID><JobId>454118</JobId></JobsID></Job> /Job/JobsID/JobId net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeConcatenate_Three_stringsInputFile0GCs0Frames0output00net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity InputFile 0 'text/plain' java.lang.String true GCs 0 'text/plain' java.lang.String true Frames 0 text/plain java.lang.String true output 0 0 workflow org.embl.ebi.escience.scuflworkers.java.StringConcat UserNameHere 2014-07-29 16:17:24.597 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeJSTWebDav3InputTokenRandGenoutJSTWebDav3InputFile_nameNoSpaceout1JSTWebDav3InputInputBodyInputBodyNoSpacestringFile_nameTargetOnlystringJSTWebDav3InputREST_Service_redirectionREST_ServicenameText_constantvalueREST_ServicemailEmailREST_ServiceargumentsConcatenate_Three_stringsoutputXPath_Servicexml_textREST_ServiceresponseBodyConcatenate_Three_stringsInputFileJSTWebDav3InputREST_Service_redirectionConcatenate_Three_stringsGCsGeneticCodeConcatenate_Three_stringsFramesFramesLogJSTWebDav3InputStatusMKDIRFileNameTargetOnlyout1JobIDXPath_ServicefirstNode b1ec8589-3ac8-4550-aa98-fb66e0661b7a 2013-03-28 09:32:22.151 UTC ca0f1d3c-efbd-488d-8abd-93fc869c9727 2013-12-12 13:56:29.479 UTC 6e506682-948f-4afd-825e-11210323a1d3 2013-06-06 14:50:47.515 UTC a2b8e237-d257-4e69-8a6c-9f030c5e5c38 2013-12-11 21:46:06.359 UTC b80541d1-48a8-4314-9512-98cb5fe1c276 2013-02-20 12:52:49.895 UTC 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8e2103e7-147d-46d5-907d-0c092f6f1da4 2014-04-13 19:12:19.224 UTC 5cfa3f7b-2671-4a85-a4b6-3f4b3e11531d 2013-12-04 16:11:00.517 UTC 8982b309-f5cd-42c8-add6-20cfbb7605cd 2014-08-07 10:43:42.100 UTC be4aa380-72a5-46cf-9f80-6afe4881de5b 2013-07-02 13:29:06.880 UTC 5dfb9d2c-95e6-415d-8c9f-847ec107140e 2013-02-19 16:37:16.674 UTC 1fe86f16-b05a-460c-a9dc-dd3b49e565d9 2014-04-13 19:12:36.822 UTC e8c5e31c-7e92-44ec-bcda-6567fea6030b 2013-12-04 11:57:56.534 UTC 28272e3a-e84b-43b1-86d1-719387da9aa6 2013-02-20 09:36:45.90 UTC a57839d6-1064-4f79-8627-c9e50655a54a 2014-07-04 09:16:53.37 UTC 83c71b7c-d10e-4508-a70b-aef98c7621de 2014-03-19 09:38:14.166 UTC a7380051-e92e-4076-9b08-7e405f1edd59 2014-03-28 16:35:11.672 UTC dbecbb79-2040-4889-b4ab-18277edb0fdb 2013-08-09 11:14:16.10 UTC BioVeL – Biodiversity Virtual e-Laboratory Workflow Documentation Name:Perform a Multiple DNA sequence alignment coding for multiple/single protein domains Capacities Programme of Framework 7: EC e-Infrastructure Programme – e-Science Environments - INFRA-2011-1.2.1 Grant Agreement No: 283359 Project Co-ordinator: Mr Alex Hardisty Project Homepage: [http://www.biovel.eu][1] [1]: http://www.biovel.eu ## 1 Description This workflow is used to submit the multiple alignment job. Once the computation is finished the user will receive an email notification indicating the obtained output address. The workflow at work translates DNA sequences following a user defined genetic code and one or more open reading frame/s. It devides the translated sequence at each stop codon into separate sequences. It searches, using hmmsearch (HMMer3.0 package), translated amino acid sequences against a mirror of PFAM-A conserved domains database. It performs a MSA of either single or multiple protein domains coding sequences. Sequences not coding for the most frequent domains order or part of it are discarded. A custom Python2.7 script retrieves then the relevant information regarding domain position falling within or on a complete sequence to align each sequence or fragment of it against its corresponding PFAM domain profile. Furthermore, all fragments are assembled to produce a multiple domain DNA alignment, by back translating protein alignments. The back-translated DNA alignments are merged together to construct the whole multiple domains alignment. ## 2 General **2.1 Name of the workflow and myExperiment +BiodiversityCatalogue identifiers** Name: Perform a Multiple DNA sequence alignment coding for multiple/single protein domains Download info: [http://www.myexperiment.org/packs/371.html][2] BiodiversityCatalogue entry: **2.2 Date, version and licensing** Last [updated:30/07/14][3] @ 16:00:00 Version: 4 Licensing: Creative Commons Attribution ShareAlike CC-BY- SA **2.3 How to cite this workflow** These results come from the processing of public data data (public repositories) through BioVeL's services ([www.biovel.eu][4]). BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359. Use the article [http://journal.embnet.org/index.php/embnetjournal/article/view/557][6] [3]: http://www.myexperiment.org/packs/371.html [4]: http://updated:21/02/13 [5]: http://www.biovel.eu [6]: http://journal.embnet.org/index.php/embnetjournal/article/view/557 ## 3. Scientific Specifications **3.1. Keywords:** MSA, coding sequences, back-translation, merger, MrBayes. **3.2. Scientific workflow description:** Arguments: 1- DNA sequences coding for single or multiple protein domain in fasta format 2- One of the following genetic codes: 1,6,10,12,15,2,3,4,5,9,13,14,16,21,22,23,11,25 3- Reading frame(s) The different step for a complete phylogenetic inference are in this pack divided as following: The email address and a filename should be provided to receive the notification of computation completion, therefore the availabilty of the results to be downloaded. ## 4. Technical Specifications **4.1. Execution environment and installation requirements** The workflows is tested in Taverna Workbench Biodiversity 2.5.0. [Taverna workbench installation][7] [7]: http://www.taverna.org.uk/download/workbench/2-5/biodiversity/ ## 5. Support For questions with using the workflow, please write [support@biovel.eu][8]. For definitions of technical and biological terms, please visit the BioVeL glossary page: [https://wiki.biovel.eu/display/BioVeL/Glossary][9] [8]: mailto:support@biovel.eu [9]: https://wiki.biovel.eu/display/BioVeL/Glossary ## 7. Bibliography 1. Donvito, G., et al. (2012) The BioVeL Project: Robust phylogenetic workflows running on the GRID. Proceedings of the EGI Community Forum 2012/EMI Second Technical Conference (EGICF12-EMITC2). 26-30 March, 2012. Munich, Germany. Published online at http://pos.sissa.it/cgi-bin/reader/conf.cgi?confid=162, id. 29. pp. 29. 2. Eddy, S.R. 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