Selecting_EvolutionaMSA_fasta00 Multiple Sequence Alignment (MSA) in fasta format 2013-02-05 15:53:08.681 UTC >ABY27676/1-453 ABY27676 ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------TTAATATTAGGA GCTCCAGATATAGCTTTTCCTCGAATAAATAATCTTAGTTTTTGGTTGCTTCCTCCTTCTTTGATTTTATTA 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--- --------- 2013-02-05 15:52:46.438 UTC PossiblePartition00 Partitioning of the MSA using nexus/raxml -like syntax 2013-02-05 15:54:20.767 UTC Gene1_pos1 = 1-657\3; Gene1_pos2 = 2-657\3; Gene1_pos3 = 3-657\3; 2013-02-05 15:53:24.969 UTC StatCriterium00 AIC 2013-12-12 11:47:51.102 UTC LinkingBranches00 linked 2013-12-12 11:47:38.808 UTC NumberRuns00 2 2013-05-16 13:42:06.19 UTC Number of independent Runs ( at least 2) [an integer] 2013-05-16 13:42:03.527 UTC MCMCMCGenerationNumber00 10000 2013-12-12 11:47:32.661 UTC Token00Path0 Path to obtain full folder of ouput of PartitionFinder 2013-02-05 15:58:50.495 UTC PartitionFinderOuput0 Best scheme according to Greedy algorithm, analysed with aic Scheme Name : 1 Scheme lnL : -3580.51738 Scheme AIC : 7267.03476 Scheme AICc : 7276.52729731 Scheme BIC : 7504.88201298 Num params : 53 Num sites : 657 Num subsets : 3 Subset | Best Model | Subset Partitions | Subset Sites | Alignment 1 | GTR+I+G | Gene1_pos1 | 1-657\3 | ./analysis/phyml/50bf1643d2a386419c9264eccd173b6b.phy 2 | GTR+G | Gene1_pos2 | 2-657\3 | ./analysis/phyml/70bf411485fb1fe3503bc4f094e24b4a.phy 3 | HKY+G | Gene1_pos3 | 3-657\3 | ./analysis/phyml/2d8c90733ab81be78313d5cf934c6639.phy Scheme Description in PartitionFinder format Scheme_1 = (Gene1_pos1) (Gene1_pos2) (Gene1_pos3); RaxML-style partition definitions DNA, p1 = 1-657\3 DNA, p2 = 2-657\3 DNA, p3 = 3-657\3 2013-02-05 15:55:19.431 UTC Text output of best model description of PartitionFinder program 2013-02-05 15:54:51.565 UTC MrBayesInput0 Input file for MrBayes in nexus format both data and model using mbayes dialect 2013-02-05 15:56:42.208 UTC #Nexus begin data; dimensions ntax=15 nchar=657; format datatype=dna interleave=no gap=- missing=? Matchchar=.; matrix ABY27676/1-453_ABY27676 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTAATATTAGGAGCTCCAGATATAGCTTTTCCTCGAATAAATAATCTTAGTTTTTGGTTGCTTCCTCCTTCTTTGATTTTATTAATAATTTCTTCAATAGTGGAGATAGGGGTTGGGGCGGGGTGAACTATTTATCCTCCTTTATCGGGTAGTCTAGGTCATTCAGGGGTTTCAGTAGATTTAGCTATTTTTAGCTTACATTTGGCGGGAGCTTCTTCAATTATAGGAGCAATTAATTTTATTTCCACTATTTTAAATATACGTTCAGTTGGGATATCTATAGATAAGGTACCTTTATTTGTGTGATCTGTATTAGTTACTGCTGTTTTATTATTATTATCTTTACCAGTTTTAGCCTGGGGTATTACGATATTATTAACAGATCGAAATTTTAACACTTCTTTTTTTGACCCTGCGGGTGGAGGTGATCCAATTTTATTTCAACATCTTTTT ADW61587/1-657_ADW61587 ACGTTATATTTAATATTTGGGGCTTGAGCTGCTATAGTAGGAACAGCCATAAGAGTATTAATTCGAATTGAATTAGGTCAACCTGGGAGGTTTATTGGGGATGATCAATTATATAATGTAATCGTTACTGCTCATGCATTTGTTATAATTTTTTTTATAGTAATACCTATTTTGATTGGAGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGCGCTCCTGATATAGCTTTTCCTCGTATAAATAATTTAAGATTTTGGCTACTCCCTCCTTCATTATTTTTATTAATTATTTCTTCTATAGTAGAAATGGGAGTGGGGGCAGGATGGACGGTTTATCCTCCTTTAGCTAGTTTAGAGGGCCATGCTGGCAGGTCAGTGGATTTTGCTATTTTTTCTTTACATTTAGCGGGGGCCTCCTCTATTATGGGGGCTATTAATTTTATTTCTACTATTATTAATATACGATCGCATGGAATAACTATAGAAAAAGTACCTTTATTTGTATGATCAGTATTGATTACTGCTGTATTATTATTATTATCACTTCCAGTATTGGCGGGGGCTATCACAATATTATTAACTGATCGAAATTTTAATACTTCGTTTTTTGACCCTTCAGGAGGGGGGGATCCAATCCTTTTCCAACATTTATTT AEE92862/1-657_AEE92862 ACGTTATATTTTGTTTTTGGAGCTTGATCTGCTATGGTAGGGACCGGAATAAGAGTAATTATTCGGTCTGAGTTGGGGCAAGTGGGGAGATTGTTGGGTGATGATCATATATATAATGTTATGGTAACTGCTCATGCTTTAGTAATGATTTTTTTTATGGTAATGCCAATCATGATTGGAGGTTTTGGTAATTGATTACTGCCTTTAATAGTAGGAGCTCCTGATATGGCTTTTCCTCGTATAAATAATTTGAGTTTTTGATTGCTTCCACCTTCTTTATTTTTGTTGGTGTTGTCTTCTTTAACAGATGTTGGGGTAGGGGCTGGTTGAACTATTTATCCTCCTTTGTCTTCGGGAGTTGGGCATGGAGGTGGGGGTATGGATTTTGCTATTTTTTCTTTGCATTTAGCTGGGGCTTCTTCTATTATGGGGGCGATTAATTTTATTACCACTATTATTAATATGCGTACAAATGGTATAACTATGGAGCGTGTGCCGTTGTTTGTGTGATCAGTATTAGTGACTGCTATTTTGTTATTATTGTCTTTACCAGTATTGGCGGGGGCTATTACGATATTACTAACAGATCGTAATTTTAATACATCTTTTTTTGATCCTGCTGGAGGAGGGGATCCTGTTCTGTTTCAGCATTTATTT AEC60810/1-657_AEC60810 ACTTTGTATTTATTGTTTGGTATTTGATCTGCTATAATGGGAACGGCAATAAGAGTGATTATTCGAATTGAATTAGGTCAAGTTGGAAGATTGTTGGGTGATGATCATTTATATAATGTAATTGTAACAGCACATGCTTTGGTTATGATTTTTTTTATAGTTATACCGATTTTGATTGGTGGATTTGGAAATTGAATAGTTCCTTTGATGTTAGGTGCTCCAGATATAGCATTCCCACGTATAAATAATTTGAGATTTTGATTGCTTCCTCCATCATTATTTTTGTTATTATTATCTTCTTTAACAGATGTAGGGGTTGGAGCCGGGTGAACTATTTATCCTCCTTTATCCTCTGGGGTTGGACATAGAGGGGGGGGGATGGATTTTGCTATTTTTTCTTTACATTTAGCAGGAGCTTCATCTATTATAGGGGCGATTAATTTTATTACAACAATTATTAATATGCGAAGATTTGGAATAACAATAGAACGTGTACCTTTATTTGTGTGATCAGTTCTTATTACTACTATTTTATTATTGCTTTCTTTACCTGTATTGGCTGGTGCTATTACTATATTGTTGACTGATCGAAATTTCAATACTTCTTTTTTTGATCCTGCTGGAGGTGGTGATCCTATTTTGTTTCAACATTTATTT AEE92861/1-633_AEE92861 ------------------------TGATCTGCTATGGTAGGTACCGGAATAAGAGTAATTATTCGGTCTGAGTTGGGGCAAGTGGGAATATTATTAGGTGATGATCATATATATAATGTTATGGTTACTGCTCATGCTTTAGTAATGATTTTTTTTATGGTAATGCCAATCATGATTGGAGGTTTTGGTAATTGATTATTGCCTTTAATGGTAGGAGCTCCTGATATGGCTTTTCCTCGTATAAATAATTTGAGTTTTTGATTGCTTCCTCCTTCTTTATTTTTGTTGGTGTTGTCTTCTTTAACAGATGTTGGGGTAGGGGCTGGTTGAACTATTTATCCTCCTTTGTCTTCGGGAGTTGGGCATGGAGGTGGGGGTATGGATTTTGCTATTTTTTCTTTGCATTTAGCTGGGGCTTCTTCTATTATGGGGGCGATTAATTTTATTACTACTATTATTAATATGCGTACAAATGGTATGACTATGGAGCGTGTGCCGTTGTTTGTGTGATCAGTATTAGTGACTGCTATTTTGTTATTGTTGTCTTTGCCAGTATTGGCGGGGGCTATTACAATATTATTGACAGATCGTAATTTTAATACATCTTTTTTTGATCCTGCTGGAGGAGGGGATCCTGTTCTGTTTCAACATTTATTT AEE92860/1-648_AEE92860 ---------TTTGTTTTTGGAGCTTGATCTGCTATGGTAGGTACCGGAATAAGAGTAATTATTCGGTCTGAGTTGGGGCAAGTGGGAAGATTATTAGGTGATGATCATATATATAATGTTATGGTTACTGCTCATGCTTTAGTAATGATTTTTTTTATGGTAATGCCAATCATGATTGGAGGTTTTGGTAATTGATTATTGCCTTTAATGGTAGGAGCTCCTGATATGGCTTTTCCTCGTATAAATAATTTGAGTTTTTGATTGCTTCCTCCTTCTTTATTTTTGTTGGTGTTGTCTTCTTTAACAGATGTTGGGGTAGGGGCTGGTTGAACTATTTATCCTCCTTTGTCTTCGGGAGTTGGGCATGGAGGTGGGGGTATGGATTTTGCTATTTTTTCTTTGCATTTAGCTGGGGCTTCTTCTATTATGGGGGCGATTAATTTTATTACTACTATTATTAATATGCGTACAAATGGTATGACTATGGAGCGTGTGCCGTTGTTTGTGTGATCAGTATTAGTGACTGCTATTTTGTTATTGTTGTCTTTGCCAGTATTGGCGGGGGCTATTACAATATTATTGACAGATCGTAATTTTAATACATCTTTTTTTGATCCTGCTGGAGGAGGGGATCCTGTTCTGTTTCAACATTTATTT ADD09384/1-555_ADD09384 ------------------------------------------------------------------------------------------------------TATCAGCTATACAATGTATTAATTACCGCTCATGCTATAATTATGGTATTTTTCATGATTATGCCAGCTTTATTTGGTGGATTTGGTAATTACTTTGTACCAATTTTAATAGGTGCCCCGGATATGGCTTTTCCTAGGCTAAATAATATAAGTTTTTGGCTACTTGTCCCTGCTTTTATATTATTAATGCTGTCAGGTTTGGTTGATGGAGGAGCTGGTACTGGCTGGACACTGTATCCTCCTCTAAGTAGTATAGTAGGGCATCCTGGCGCTGCTGTCGATATGGCTATTTTAAGCTTACATCTTACAGGGCTTTCCTCCATTCTTGGTTCAATTAATATGATTGTCACTATCTTTAATATGAGAACTGATGGTATGGGGTTATTTGAAATGCCCTTATTTGTTTGGTCAATTTTGGTTACTGCCTTCTTGCTGATACTAGCAATTCCTGTGTTAGGGGGTGCAATAACCATGTTACTGACTGATCGAAATTTTGGTACTACTTTTTTCAAGCCTGATGGTGGCGGAGATCCAGTGTTATTTCAGCATTTATTT ADJ82639/1-645_ADJ82639 ACTTTATATTTAATGTTTGGGGTTTGGTCAGCTATAATAGGAACTGCTATAAGAGTATTAATTCGAATGGAATTAGGGAATCCTGGTAGATTGTTAGGTGATGATCATTTGTATAATGTTATAGTTACTGCTCATGCTTTTGTAATAATTTTTTTTATAGTAATGCCTATTCTTATTGGAGGTTTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCAGATATATCATTTCCTCGAATAAATAATCTTTCTTTTTGATTATTACCTCCTTCTTTATTTTTGTTATCTATATCTTCTATAGTAGAAATAGGAGTTGGGGCTGGGTGAACTGTTTATCCTCCTTTAGCGTCTACAGTTGGGCACATAGGAAATTCAATAGATTTTGCTATTTTTTCTCTTCATTTAGCTGGAGCTTCTTCTATTATAGGAGCTGTAAATTTTATTTCTACCATTATTAATATACGAATATTAGGAATATCTATAGAGAAGGTTCCTCTTTTTGTTTGATCAGTTTTAATTACAGCAGTATTATTATTACTTTCTTTACCTGTTTTAGCAGGTGCTATTACTATATTATTAACAGATCGAAATTTTAATACTTCTTTTTTTGATCCTGCTGGGGGAGGAGATCCTAATTTATTT------------ ADQ21240/1-648_ADQ21240 AGATTATATTTTGTTTTTGGGGCTTGAGCTGCTATAGTAGGAACAGCAATAAGAGTATTAATTCGTGTTGAGTTGGGACAAACTGGTAGTTTGTTAGGGGATGATCAGTTGTATAATGTTATTGTTACGGCTCATGCTTTTGTAATAATTTTTTTTATAGTTATGCCTATTTTAATTGGGGGTTTTGGAAATTGGCTGATTCCACTAATACTAGGAGCTCCGGATATAGCTTTCCCTCGTATAAATAATTTGAGATTTTGGCTTTTACCCCCTTCTTTATTATTACTGTTTATTTCAAGCATAGATGAGATAGGAGTGGGGGCGGGATGAACGGTTTACCCCCCTCTTGCCTCTTTAGAGGGACATTCTGGTAGTTCAGTAGATTTTGCTATTTTTTCTTTACACTTAGCTGGAGCGTCTTCTATTATAGGGGCTATTAATTTTATTTCCACAATTTTGAATATACGGGGTTATGGAATATCTATAGAAAAAGTACCTTTATTTGTTTGGTCCGTGTTAATTACAGCTGTATTATTATTGTTATCTCTTCCTGTGTTAGCTGGGGCTATCACAATATTACTGACGGATCGTAATTTTAATACTTCATTTTTTGATCCTTGTGGGGGGGGGGATCCTGTTTTGTTTCAA--------- AEE92882/1-657_AEE92882 ACGTTATATTTTGTTTTTGGAGCTTGATCTGCTATGGTAGGGACCGGAATAAGAGTAATTATTCGGTCTGAGTTGGGGCAAGTGGGGAGATTGTTGGGTGATGATCATATATATAATGTTATTGTAACTGCTCATGCTTTAGTAATGATTTTTTTTATGGTAATGCCAATCATGATTGGAGGTTTTGGTAATTGATTACTGCCTTTAATAGTAGGAGCTCCTGATATGGCTTTTCCTCGTATAAATAATTTGAGTTTTTGATTGCTTCCACCTTCTTTATTTTTGTTGGTGTTGTCTTCTTTAACAGATGTTGGGGTAGGGGCTGGTTGAACTATTTATCCTCCTTTGTCTTCGGGAGTTGGGCATGGAGGTGGGGGTATGGATTTTGCTATTTTTTCTTTGCATTTAGCTGGGGCTTCTTCTATTATGGGGGCGATTAATTTTATTACCACTATTATTAATATGCGTACAAATGGTATAACTATGGAGCGTGTGCCGTTGTTTGTGTGATCAGTATTAGTGACTGCTATTTTGTTATTATTGTCTTTACCAGTATTGGCGGGGGCTATTACGATATTACTAACAGATCGTAATTTTAATACATCTTTTTTTGATCCTGCTGGAGGAGGGGATCCTGTTCTGTTTCAGCATTTATTT ADW58691/1-657_ADW58691 ACTTTATATTTAATATTTGGAGCTTGATCTGCTATAGTAGGGACTGCTATAAGAGTGTTAATTCGAATAGAATTAGGTCAATCTGGAAGACTTTTAGGTGATGATCATTTATATAATGTTGTAGTTACTGCACATGCTTTTGTTATAATTTTTTTTATAGTTATACCTATTTTGATTGGTGGTTTTGGAAATTGGTTAGTTCCTTTAATATTAGGTGCTCCTGATATAGCTTTTCCTCGAATAAATAATTTAAGTTTTTGATTATTACCTCCTTCTTTATTTTTATTATTTATTTCTTCTATAGTTGAAATAGGAGTTGGAGCAGGATGAACAGTTTATCCTCCATTGGCATCTAGTGTAGGTCATATGGGAAGTGCAATAGATTTTGCTATTTTTTCATTACATTTGGCTGGTGCTTCTTCTATTATAGGAGCAGTAAATTTTATTACTACTATTATTAATATACGTTCTCATGGAATAAGAATAGAAAAAGTTCCTTTATTTGTTTGATCAGTTTTAATTACAGCTATTTTGTTGTTATTATCTTTACCTGTTTTAGCAGGTGCTATTACTATATTATTAACTGATCGTAATTTTAATACTTCTTTTTTTGATCCTGCTGGAGGAGGAGATCCTATTTTATTTCAACATTTATTT ADW58631/1-657_ADW58631 ACTTTATATTTAATATTTGGAGCTTGATCTGCTATAGTAGGGACTGCTATAAGAGTGTTAATTCGAATAGAATTAGGTCAATCTGGAAGACTTTTAGGTGATGATCATTTATATAATGTTGTAGTTACTGCACATGCTTTTGTTATAATTTTTTTTATAGTTATACCTATTTTGATTGGTGGTTTTGGAAATTGGTTAGTTCCTTTAATATTAGGTGCTCCTGATATAGCTTTTCCTCGAATAAATAATTTAAGTTTTTGATTACTACCTCCTTCTTTATTTTTATTATTTATTTCTTCTATAGCTGAAATAGGAGTTGGAGCAGGATGAACAGTTTATCCTCCATTGGCATCTAGTGTAGGTCATATAGGAAGTGCAATAGATTTTGCTATTTTTTCATTACATTTGGCTGGTGCTTCTTCTATTATAGGAGCAGTAAATTTTATTACTACTATTATTAATATACGTTCTCATGGAATAAGAATAGAAAAAGTTCCTTTATTTGTTTGATCAGTTTTAATTACAGCTATTTTGTTGTTATTATCTTTACCTGTTTTAGCAGGTGCTATTACTATATTATTAACTGATCGTAATTTTAATACTTCTTTTTTTGATCCTGCTGGAGGAGGAGATCCTATTTTATTTCAACATTTATTT ACM89220/1-657_ACM89220 ACTTTATATTTTTTATTTGGTACTTGATCAGCAATAATTGGTACAGCAATAAGTGTTTTAATTCGTGTTGAACTAGGATTTTCTGGAAGATTTTTAGGTGATGATCATTTATATAATGTAATTGTTACTGCTCATGCTTTTATTATAATTTTTTTTATAGTTATACCTATTTTAATTGGTGGTTTTGGAAATTGGTTAGTTCCTTTAATATTAAGAGCTCCAGATATAGCTTTTCCTCGTATAAATAATTTAAGATTTTGGTTACTACCTCCTTCGTTATTATTGTTATTTATTTCTTCTATGGTTGAAATCGGAGTTGGAGCAGGGTGGACTATTTATCCTCCTTTATCTTCTTCTGTGGGTCATTCTGGTGCATCTATGGATTTTGCAATTTTTTCTCTTCATTTAGCTGGTGCTTCTTCTATTATAGGTGCTATTAATTTTATTTCAACAATTATTAATATACGACCTTATGGTATAAGAATAGAAAAGATTCCTTTATTTGTATGATCTGTATTAATTACAGCTGTCTTATTATTATTATCATTACCAGTATTAGCTGGGGCTATTACTATACTTTTAACTGATCGTAATTTTAATACTTCTTTTTTTGATCCAGCTGGGGGTGGGGATCCAATTTTATTTCAGCATTTATTT AEE92867/1-642_AEE92867 ---------------TTTGGGGCTTGATCTGCTATGGTAGGTACCGGAATAAGAGTAATTATTCGGTCTGAGTTGGGGCAAGTGGGAAGATTATTAGGTGATGATCATATATATAATGTTATGGTTACTGCTCATGCTTTAGTAATGATTTTTTTTATGGTAATGCCAATCATGATTGGAGGTTTTGGTAATTGATTATTGCCTTTAATGGTAGGAGCTCCTGATATGGCTTTTCCTCGTATAAATAATTTGAGTTTTTGATTGCTTCCTCCTTCTTTATTTTTGTTGGTGTTGTCTTCTTTAACAGATGTTGGGGTAGGGGCTGGTTGAACTATTTATCCTCCTTTGTCTTCGGGAGTTGGGCATGGAGGTGGGGGTATGGATTTTGCTATTTTTTCTTTGCATTTAGCTGGGGCTTCTTCTATTATGGGGGCGATTAATTTTATTACTACTATTATTAATATGCGTACAAATGGTATGACTATGGAGCGTGTGCCGTTGTTTGTGTGATCAGTATTAGTGACTGCTATTTTGTTATTGTTGTCTTTGCCAGTATTGGCGGGGGCTATTACAATATTATTGACAGATCGTAATTTTAATACATCTTTTTTTGATCCTGCTGGAGGAGGGGATCCTGTTCTGTTTCAACATTTATTT ADH12119/1-645_ADH12119 ACTTTATACTTGGTTTTTGGTGCTTGAGCGGCTATGGTTGGAACTGCAATAAGTGTTTTAATTCGAATTGAGTTGGGGCAATCTGGTAGATTTATGGGAGATGATCAGTTGTATAATGTTATTGTAACTGCTCATGCTTTTGTTATAATTTTTTTTATGGTTATGCCTATTTTGATTGGGGGCTTTGGTAATTGACTGGTTCCTTTGATGTTGGGGGCTCCTGATATGGCTTTTCCTCGCATGAATAATTTAAGGTTTTGATTATTGCCTCCTTCTTTATTTTTATTATTTATTTCTTCTATGGTGGAAATAGGGGTTGGGGCTGGTTGAACGATCTACCCTCCTTTAGCGTCTCTAGAAGGACATTCAGGAAGTTCGGTTGATTTTGCCATTTTTTCTTTGCATTTGGCTGGGGCCTCTTCTATTATAGGGGCTATTAATTTTATTTCTACAATTTTGAATATACGGTCTTATGGGATGTCTATGGAAAAAGTTCCTTTGTTTGTTTGGTCGGTTTTAATTACTGCTGTTTTGCTCCTATTATCACTTCCGGTTTTAGCTGGGGCTATCACTATGTTATTAACTGATCGAAATTTTAATACATCGTTTTTTGATCCTTCGGGGGGAGGGGATCCTATTTTTTTT------------ ; end; begin mrbayes; set autoclose=yes; charset Gene1_pos1 = 1-657\3; charset Gene1_pos2 = 2-657\3; charset Gene1_pos3 = 3-657\3; charset p1 =Gene1_pos1; charset p2 =Gene1_pos2; charset p3 =Gene1_pos3; partition current_partition =3:p1, p2, p3; Lset applyto=(1) rates=invgamma nst=6; Lset applyto=(2) rates=gamma nst=6; Lset applyto=(3) rates=gamma nst=2; link Brlens=(all); unlink statefreq=(all); unlink shape=(all); link topology=(all); end; 2013-02-05 15:57:07.212 UTC Log0Call_PartitionFinderName0Argument0JobID00Standardoutput00Output_Path00StandardError00net.sf.taverna.t2.componentcomponent-activity1.5net.sf.taverna.t2.component.ComponentActivity http://www.myexperiment.org JSTInteraction JSTAsync2 7 The Workflow allow a robust asynchronous interaction with Job submission Tool of INFN. 2014-01-21 12:57:06.737 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.InvokeServiceNamevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity PartitionFinder 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_two_stringsstring20string10output00net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity string1 0 'text/plain' java.lang.String true string2 0 'text/plain' java.lang.String true output 0 0 workflow org.embl.ebi.escience.scuflworkers.java.StringConcat UserNameHere 2013-01-30 10:36:22.209 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.InvokeFile_name_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity partition_finder.cfg 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.InvokeFile_name_value_1value00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity test.phy 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.InvokeModelsetGUIGenePartition0StatCriterium0LinkingBranch0PartitionDef00BL00Test00net.sf.taverna.t2.activitiesdataflow-activity1.5net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.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.InvokeMrBayesParserBL0PartDef0PartFinder0MSAphy0nGen0nRun0MrBayesBlock00net.sf.taverna.t2.activitiesexternal-tool-activity1.5net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation> 8736e2c3-d3eb-4fa2-957e-0f48330eab36 python PartitionParser.py PartDef PartFinder %%BL%% MSAphy %%nGen%% %%nRun%% 1200 1800 BL nGen nRun PartitionParser.py true false false UTF-8 false def phy2mrbayes(phy, DNA=True): A=open(phy,"r").readlines() ntaxa, nseq=A[0].split() A=[x.split()[0].replace("/","_").replace("-","_")+" "+x.split()[1]+"\n" for x in A[1:]] phylip="phylip format requires that first line includes only two integers" assert int(ntaxa), phylip assert int(nseq), phylip assert DNA, "program assume sequence are nucleotides" header= '#Nexus\n\nbegin data;\ndimensions ntax={ntaxa} nchar={nseq};\nformat datatype=dna interleave=no gap=- missing=? Matchchar=.;\nmatrix\n'.format(ntaxa=ntaxa,nseq=nseq) footer=";\nend;\n" return header+"".join(A)+footer def PartitionFinder2MrBayes(PartDef, PartFinder, brlink, ngen, nrun ): matrix={"JC":"1", "F81":"1", "K80":"2", "HKY":"2", "SYM":"6", "GTR":"6"} SS={"+I":"inv","+G":"gamma","+I+G":"invgamma","":"equal"} pi={"JC":"fixed(equal)", "F81":"Dirichlet(1.0,1.0,1.0,1.0)", "K80":"fixed(equal)", "HKY":"Dirichlet(1.0,1.0,1.0,1.0)", "SYM":"fixed(equal)", "GTR":"Dirichlet(1.0,1.0,1.0,1.0)"} footer="unlink statefreq=(all);\nunlink shape=(all);\nlink topology=(all);\nmcmcp ngen="+ngen+ " samplefreq=100 nchains=16 temp=0.200000 nruns="+nrun+";\nmcmc;\nquit;\nend;\n" header="begin mrbayes;\nset autoclose=yes;\n\n" Part=open(PartDef,"r").readlines() Part=["charset "+i for i in Part] flag=False #Subsets={} char="" mod="" for i in open(PartFinder,"r"): line=i.split() if len(line)==0: continue #print(line) if flag: l=[j.strip() for j in i.split("|")] if len(l)==1: break npartition=int(l[0]) Model=l[1] Model=Model.split("+") M=matrix[Model[0]] if M=="6": footer="unlink Revmat=(all);\n"+footer elif M=="2": footer="unlink Tratio=(all);\n"+footer if len(Model)>1: ss=SS["+"+Model[1]] else: ss=SS[""] #Subsets[line[0]]={model:line[1],sets:line[2]} groupdef=" ".join(l[2].split(", ")) char+="charset p"+l[0]+" ="+groupdef+";\n" mod+="Lset applyto=("+l[0]+") rates="+ss+" nst="+M+";\n" elif line[0]=="Subset": flag=True BL="unlink Brlens=(all);\n" if flag: char+="partition current_partition ="+str(npartition)+":"+", ".join(["p"+str(i+1) for i in range(npartition)])+";\n" char+="set partition = current_partition;\n" if brlink=="linked": BL="link Brlens=(all);\n" return header+"".join(Part)+"\n"+char+mod+BL+footer if "__main__"==__name__: import sys temp=PartitionFinder2MrBayes(sys.argv[1],sys.argv[2],sys.argv[3], sys.argv[5], sys.argv[6]) temp1=phy2mrbayes(sys.argv[4]) handle=open("MrBayesBlock","w") handle.write(temp1) handle.write(temp) handle.close() nGen nGen false false false UTF-8 false false false PartFinder PartFinder true false false UTF-8 false false false MSAphy MSAphy true false false UTF-8 false false false nRun nRun false false false UTF-8 false false false PartDef PartDef true false false UTF-8 false false false BL BL false false false UTF-8 false false false MrBayesBlock MrBayesBlock false false true true 0 false 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.Invokefasta2phyMSAfasta0MSAphy00net.sf.taverna.t2.activitiesexternal-tool-activity1.5net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation> c8c06e00-9f5a-464d-9e4e-9deb4eab8f4d python Fasta2Phy.py MSAfasta 1200 1800 Fasta2Phy.py true false false MacRoman false def Fasta2Phy(MSAfasta): msa=open(MSAfasta,"rU").readlines() msa="\n".join([i.strip() for i in msa]) records=[(i[:i.find("\n")].replace(" ","_").translate(None,"'|@#"),i[i.find("\n"):].replace("\n","").strip()) for i in msa.split(">")[1:]] ntaxa=len(records) nseq=len(records[0][1]) assert all([len(i[1])==nseq for i in records]), "all records should have same length" body="\n".join([i[0]+" "+i[1] for i in records]) return " ".join(map(str,(ntaxa,nseq)))+"\n"+body+"\n" if "__main__"==__name__: import sys out=Fasta2Phy(sys.argv[1]) handle=open("MSAphy","w") handle.write(out) handle.close() MSAfasta MSAfasta true false false MacRoman false false false MSAphy MSAphy false false true true 0 false 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.InvokeLoggerJobID0Name0StdError0output00net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity Name 0 'text/plain' java.lang.String true JobID 0 'text/plain' java.lang.String true StdError 0 text/plain java.lang.String true output 0 0 workflow org.embl.ebi.escience.scuflworkers.java.StringConcat UserNameHere 2013-06-14 14:20:10.140 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 2 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeJSTWebDav3InputFile_name0InputBody0Token0REST_Service_redirection00net.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.InvokeJSTWebDav3Input_2File_name0Token0InputBody0REST_Service_redirection00net.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.InvokeMerge_String_List_to_a_Stringstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge 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.InvokeCall_PartitionFinderNameServiceNamevalueCall_PartitionFinderArgumentConcatenate_two_stringsoutputConcatenate_two_stringsstring2JSTWebDav3InputREST_Service_redirectionConcatenate_two_stringsstring1JSTWebDav3Input_2REST_Service_redirectionModelsetGUIGenePartitionPossiblePartitionModelsetGUIStatCriteriumStatCriteriumModelsetGUILinkingBranchLinkingBranchesMrBayesParserBLModelsetGUIBLMrBayesParserPartDefModelsetGUIPartitionDefMrBayesParserPartFinderCall_PartitionFinderStandardoutputMrBayesParserMSAphyfasta2phyMSAphyMrBayesParsernGenMCMCMCGenerationNumberMrBayesParsernRunNumberRunsfasta2phyMSAfastaMSA_fastaLoggerJobIDCall_PartitionFinderJobIDLoggerNameServiceNamevalueLoggerStdErrorCall_PartitionFinderStandardErrorJSTWebDav3InputFile_nameFile_name_valuevalueJSTWebDav3InputInputBodyModelsetGUITestJSTWebDav3InputTokenTokenJSTWebDav3Input_2File_nameFile_name_value_1valueJSTWebDav3Input_2TokenTokenJSTWebDav3Input_2InputBodyfasta2phyMSAphyMerge_String_List_to_a_StringstringlistLoggeroutputPathCall_PartitionFinderOutput_PathPartitionFinderOuputCall_PartitionFinderStandardoutputMrBayesInputMrBayesParserMrBayesBlockLogMerge_String_List_to_a_Stringconcatenated dcceda48-bbd8-44d2-8c62-8d246788ca2b 2014-11-25 16:22:18.826 UTC 6d66ed79-a12a-4241-b18b-c498a7d2da07 2013-02-01 14:57:44.153 UTC 07d67623-09a9-4cf4-8407-e7e1f5edf511 2013-06-06 14:48:54.705 UTC 69c8c748-98a3-4031-a1c4-e5fa4b09b601 2013-02-05 13:23:51.883 UTC saverio vicario giacinto donvito 2013-02-01 14:55:26.151 UTC 533616aa-30cd-40e1-8fc8-66b1fb68a5f2 2013-05-17 13:46:11.29 UTC ece44cfb-3667-4f51-9318-d7e6451319a9 2013-02-18 17:03:00.532 UTC aa7672fb-a133-4368-a70f-776d1805f14a 2013-03-28 09:12:56.224 UTC 3ee4ded3-e029-4559-babb-052d82632904 2013-12-04 11:46:31.602 UTC 625baf1c-821f-44df-9ce4-63f172c0f7ee 2013-01-30 16:08:31.899 UTC d4627728-1123-443c-ae77-a80f54648782 2013-02-07 15:22:17.514 UTC 2ed8c1a7-e451-469a-a46a-11239145da5a 2013-02-05 15:45:49.815 UTC ec00f016-0fc9-4241-9ab6-848823bd4c3f 2013-12-11 13:39:27.136 UTC 9e6923d1-a6aa-43ce-bffb-fa7aee07dff9 2013-02-19 10:42:25.870 UTC 0258f22b-486e-4dfb-a718-ab420717d865 2013-01-30 10:36:25.295 UTC 6a29d91a-01d6-4f61-b437-fb66453b7f8c 2013-01-30 16:22:17.814 UTC 30ad3239-4489-4335-afbe-2ed9eb1dd905 2014-01-21 16:47:28.560 UTC 10cd9e3a-e4b7-4871-97a0-7b84601bc1ca 2013-03-28 11:31:47.181 UTC 36508d52-f6c4-4b5a-a107-c6f711555e62 2013-05-16 12:50:57.208 UTC bbafafab-5998-4370-b8bf-d3465859a610 2014-01-22 16:29:29.923 UTC 622bbc0f-ba1b-4f9f-b8f6-c1296931c721 2013-02-18 17:11:04.467 UTC 62c2d85e-9e96-4d18-bb3c-e17891539a6d 2013-06-14 15:24:38.838 UTC 86d5f93b-05de-4202-90f0-ec91a695cff4 2013-02-05 16:02:05.335 UTC 23b9c9df-a159-48b2-a5be-63d45120e616 2013-03-28 11:12:26.809 UTC 878abc7e-b91f-411b-86fc-f586a420a7fa 2013-02-08 16:05:33.86 UTC 9a53f85f-1c88-4986-bbf4-69e15a239924 2013-12-16 14:32:08.638 UTC f65b5110-abee-45c8-9881-a02842f5ed9f 2013-03-28 08:09:47.207 UTC 5cd1547e-b30b-44e2-a6d3-2fe26acf61c4 2013-02-18 18:54:37.560 UTC b11ccf00-aa73-48b0-927b-8d4ab1d845cf 2013-01-30 10:15:32.989 UTC 7597c8f7-80d3-4b3b-a269-1e09797498e2 2013-02-05 14:44:06.990 UTC 2c58afd6-20a3-424d-9ed7-038e197bbebc 2013-12-17 15:39:20.941 UTC 49732954-164b-4bef-b599-d5a14f5da540 2013-02-18 15:11:55.137 UTC c87599a9-53f3-4f71-aa9d-a52fa46d6150 2013-02-18 17:28:31.184 UTC 28c91d66-2c4a-476d-8d78-db869b453921 2013-02-18 22:01:20.399 UTC 1d9f99b9-2483-492d-aefe-04cd24d0f3fc 2013-03-28 09:32:12.303 UTC 784b60fc-f91f-4a16-a624-feb77ace8d10 2013-02-05 08:21:09.643 UTC 866e4caf-7829-437c-b6a7-dcf0a48cd588 2013-02-07 16:17:46.706 UTC 1a9c1703-b237-42f3-b12d-d6c12c660e17 2014-01-10 15:56:43.277 UTC aacc5e27-15e1-4f78-be93-da93151f35d2 2013-02-18 16:03:05.530 UTC 0a1d0617-99c6-4584-99a7-9263a40958cf 2013-12-12 11:46:04.725 UTC f8f164be-ffd1-4937-b5b4-8c4e1fb3ccf0 2013-01-30 11:17:44.316 UTC 4535d120-69bc-4724-bae2-5b51a7d263a4 2014-05-12 12:14:40.89 UTC 1d19ca77-9351-4595-ab58-24ab59ff26c0 2013-01-30 16:23:36.508 UTC d80548e2-8a32-4520-a6a0-429ef1db1244 2013-01-30 16:14:06.707 UTC bcf4637b-1d4a-4240-bdd8-4b5af36e7e46 2014-01-28 11:03:40.484 UTC 863e00c4-6cc6-4979-9acd-f720b98d7c86 2013-02-05 13:30:10.377 UTC Selecting Evolutionary Model for a phylogenetic inference using partitionFinder program. The program (http://www.robertlanfear.com/partitionfinder/) search best candidate model that satisfy need of the different partition. The program do not explore all possible model that could be implemented in mrbayes, in fact it do not allow for link of subsitution matrix but different base frequency across partitions, or to link branch lenght across some partitions but not all. For a greater fine tuning of model the user is advised to use the GUI interface present in the phylogenetic inference pipeline 2013-02-05 16:02:01.665 UTC ff724eeb-cedc-411f-8d38-9602e06fe5e5 2013-05-17 13:17:05.788 UTC c08ff261-ed08-4fd2-bf0c-e1d537fe0e48 2014-11-25 16:42:17.417 UTC e23aad11-3744-4901-830c-4a4b3d646eb7 2013-02-05 07:55:19.124 UTC 460ddb89-37f9-4fd5-858b-2c7e7e5b84f1 2013-12-17 15:56:15.927 UTC 67a1c1f6-1e36-47c2-8336-45deea5ed4e2 2013-05-16 12:55:54.77 UTC 777979a6-ecf0-48a8-a328-7bffd3efdb8c 2013-02-07 16:19:51.911 UTC 9ac94254-0a2a-40c3-8d40-22901e8489cc 2014-01-22 16:54:27.42 UTC b1d9331f-cd10-4706-a80e-e46cdceb2a3d 2013-12-04 14:54:27.24 UTC 45591344-1d68-4777-aef1-e3dc645624b5 2013-02-05 10:43:14.770 UTC 0ed7ac93-3ba3-4710-9f47-9639ed7f1641 2013-02-05 15:37:30.903 UTC 7e3af809-4836-4038-b76d-19d3698937ca 2013-12-17 15:43:15.327 UTC Selecting Evolutionary Model for a phylogenetic inference using partitionFinder program 2013-02-05 15:59:05.888 UTC f962b042-4d38-4192-a46d-b42669ee1ed6 2013-02-07 15:25:41.898 UTC 8571e775-ce55-4c58-b86d-81b82dd7271e 2013-03-28 11:24:22.676 UTC b721c886-a987-41f0-a161-229785ca2ee4 2013-12-17 15:04:09.773 UTC 6b59ee47-001c-487b-bad5-5496aef788fc 2013-01-30 11:14:31.315 UTC 7263a20c-e25e-4de8-a1c0-0d4e74d184a3 2013-12-02 16:54:29.556 UTC 24112111-8abf-4ffa-a503-57a6a1594a09 2013-02-05 15:11:07.370 UTC 6cfda8b0-06aa-4e11-a0ff-5c12e525d978 2013-02-05 09:13:41.823 UTC 73e0f222-ba61-4c33-b351-37ec2004695f 2013-02-05 14:03:46.335 UTC 273e5c0b-5007-4ea5-83f3-6aa9a942a191 2013-02-05 14:13:04.454 UTC a5b4f767-dc5c-49f1-bb89-7ec6892d1e7c 2013-12-04 16:09:43.325 UTC e34617cf-01cc-44bf-81fa-4cfbe968b63e 2013-03-28 09:13:52.739 UTC 46fa7fa8-9840-48c1-86a7-b14ba3d73c8d 2013-05-16 13:07:04.101 UTC a13c0e71-3e62-4ba5-be4c-007188740620 2013-03-27 14:49:25.87 UTC 150d8989-b40f-4f7f-92b7-c60657ab248e 2013-06-14 14:35:58.682 UTC fb26e251-b8e2-44f6-95ee-c90b32dec278 2013-02-18 17:16:29.896 UTC 69d2952c-d3b1-4310-97b6-d742626fa971 2013-02-18 15:53:17.645 UTC 427ea715-e2b7-4768-967b-1b3e188e1d4d 2013-05-16 13:44:54.639 UTC aefd0acd-4497-4bfc-b66b-8ba2c230a966 2013-01-30 11:19:45.253 UTC c610171a-5757-4944-acc2-fb83323cffbd 2013-01-30 10:34:01.370 UTC 3bfd589f-8584-4288-8ab3-49117e9dbdff 2013-12-11 13:43:57.470 UTC 80768ac7-2051-474c-b6ca-84b3db44164e 2013-01-30 13:45:25.256 UTC 561e9fc2-e9bb-4b7b-8a38-c83dbaff7f3e 2013-05-17 13:42:47.78 UTC 02689531-43df-4117-a26d-7c905f615d47 2013-12-12 11:48:11.805 UTC 8d886d36-113b-49b5-a914-930884e04bb5 2013-02-05 13:36:43.166 UTC Workflow1GenePartition00 Gene1_pos1 = 1-789\3; Gene1_pos2 = 2-789\3; Gene1_pos3 = 3-789\3; Gene2_pos1 = 790-1449\3; Gene2_pos2 = 791-1449\3; Gene2_pos3 = 792-1449\3; Gene3_pos1 = 1450-2208\3; Gene3_pos2 = 1451-2208\3; Gene3_pos3 = 1452-2208\3; 2012-11-12 15:44:26.975 UTC LinkingBranch00 linked 2013-05-16 13:35:00.679 UTC Does models should assume branch in the tree linked or unlinked across partition. Two possible strings: linked unlinked 2013-05-16 13:34:51.834 UTC StatCriterium00 AIC 2013-05-16 13:38:52.915 UTC What statistical criterium should be used to compare different models? AIC = Aikake information Criterium AICc =Aikake information Criterium correct per sample size BIC = Bayesian Information Criterium 3 possible values: AIC, AICc, or BIC 2013-05-16 13:38:48.836 UTC Test0PartitionDef0BL0AddLinestring10string20output00net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity string1 0 'text/plain' java.lang.String true string2 0 'text/plain' java.lang.String true output 0 0 workflow org.embl.ebi.escience.scuflworkers.java.StringConcat UserNameHere 2012-11-12 16:07:38.633 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.InvokeText_constant_2value00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity alignment = test.phy; 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.InvokeAddLine_2string10string20output00net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity string1 0 'text/plain' java.lang.String true string2 0 'text/plain' java.lang.String true output 0 0 workflow org.embl.ebi.escience.scuflworkers.java.StringConcat UserNameHere 2012-11-12 16:09:44.412 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.InvokeAddLine_2_2string10string20output00net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity string1 0 'text/plain' java.lang.String true string2 0 'text/plain' java.lang.String true output 0 0 workflow org.embl.ebi.escience.scuflworkers.java.StringConcat UserNameHere 2012-11-12 16:09:57.482 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.InvokeSplit_string_into_string_list_by_regular_expression_2_2_2regex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex UserNameHere 2013-05-16 13:02:35.786 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.Invokeregex_value_1value00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity ;[\n\r]* 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.InvokeAddLine_2_2_2string10string20output00net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity string1 0 'text/plain' java.lang.String true string2 0 'text/plain' java.lang.String true output 0 0 workflow org.embl.ebi.escience.scuflworkers.java.StringConcat UserNameHere 2012-11-12 16:05:42.919 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.InvokeConcatenate_two_stringsstring10string20output00net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity string1 0 'text/plain' java.lang.String true string2 0 'text/plain' java.lang.String true output 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringConcat 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.Invokestring1_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity branchlengths = 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_two_strings_2string10string20output00net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity string1 0 'text/plain' java.lang.String true string2 0 'text/plain' java.lang.String true output 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringConcat 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.Invokestring1_value_1value00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity models = 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_two_strings_2_2string10string20output00net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity string1 0 'text/plain' java.lang.String true string2 0 'text/plain' java.lang.String true output 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringConcat 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.Invokestring1_value_2value00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity model_selection = 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.InvokeFlatten_Listinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList 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.InvokeMerge_String_List_to_a_Stringstringlist1seperator0concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge 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.Invokeseperator_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 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.Invokemessage_value_3net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity What partitions should be taken in consideration? Check that partitions are not overlapping. 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.Invokestring2_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity mrbayes 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.InvokeAddLinestring1Text_constant_2valueAddLinestring2Concatenate_two_stringsoutputAddLine_2string1AddLineoutputAddLine_2string2Concatenate_two_strings_2outputAddLine_2_2string1AddLine_2outputAddLine_2_2string2Concatenate_two_strings_2_2outputSplit_string_into_string_list_by_regular_expression_2_2_2regexregex_value_1valueSplit_string_into_string_list_by_regular_expression_2_2_2stringGenePartitionAddLine_2_2_2string1AddLine_2_2outputAddLine_2_2_2string2Merge_String_List_to_a_StringconcatenatedConcatenate_two_stringsstring1string1_valuevalueConcatenate_two_stringsstring2LinkingBranchConcatenate_two_strings_2string1string1_value_1valueConcatenate_two_strings_2string2string2_valuevalueConcatenate_two_strings_2_2string1string1_value_2valueConcatenate_two_strings_2_2string2StatCriteriumFlatten_ListinputlistSplit_string_into_string_list_by_regular_expression_2_2_2splitMerge_String_List_to_a_StringstringlistFlatten_ListoutputlistMerge_String_List_to_a_Stringseperatorseperator_valuevalueTestAddLine_2_2_2outputPartitionDefMerge_String_List_to_a_StringconcatenatedBLLinkingBranch 9e91858b-9426-48b9-a804-644955ec199e 2012-11-12 08:22:58.858 UTC 7301d737-5a02-448e-9c2e-593e534260fa 2012-11-12 08:24:05.103 UTC 71d05d02-28f6-4243-8698-fd54f052a798 2013-05-16 12:55:48.422 UTC 63e1dc68-96a5-492e-9c8b-0d44e0133425 2013-05-17 13:42:20.937 UTC 0c74aa00-88fe-4054-8a36-fe079271288b 2013-02-18 14:47:57.525 UTC 5358b2f1-c19e-4931-a3cd-c5c370f8733a 2013-05-16 13:40:13.704 UTC 954cd73a-9f79-4ee2-af0d-afd5b11f9c77 2013-05-16 13:02:57.781 UTC 5295583d-9241-4c02-9979-4c2e86ba3925 2013-02-01 17:23:06.830 UTC 260e8787-b99b-4c27-8f7f-ba635c81a2d3 2013-12-17 15:55:55.696 UTC fb12cc76-5149-4ab6-8672-9925934d28e3 2012-11-14 11:58:50.736 UTC 56efae61-d700-404c-ae00-917990e6f177 2012-11-14 11:42:15.476 UTC 1f8a34d0-dc3b-4b1c-b137-b046eda1474f 2012-11-12 16:08:46.864 UTC 7861a683-4ce4-46a3-b3df-244b1e8f71d5 2013-02-05 09:47:42.150 UTC f56367cd-8876-40d9-b0e0-45502d85c6a0 2013-01-30 09:04:48.43 UTC 2c56084c-7ca2-477f-9aef-856c9a8b520f 2013-05-16 12:50:53.334 UTC 3f130b52-a27d-46e1-bf95-0b8901491a21 2013-02-05 07:57:16.896 UTC f2abe179-d96a-4d3b-9e4a-a360a9030520 2012-11-12 15:19:19.643 UTC 6957a2cb-0985-4c20-94b7-31075e70f908 2012-11-12 16:10:04.480 UTC 95f8af6c-8196-4505-b7eb-33ce41d2ce96 2014-01-28 11:02:09.561 UTC cfb3e923-7c55-4f0a-bf14-569bd22cc752 2012-11-12 16:14:10.632 UTC 70d3be26-9ac3-4d0b-a1ea-54be33c25866 2013-01-30 09:12:57.275 UTC bea60039-1487-408e-ab7f-ae9fbf3d0e26 2012-11-12 15:32:00.915 UTC 097e1982-0bac-4a21-b3a8-d7767c39fe23 2012-11-12 15:29:11.584 UTC 5bed52c2-7274-42c2-ba5c-602a84244b10 2013-01-30 09:14:54.76 UTC 437e3da5-f933-4b84-adee-f7b15d2be6a7 2013-01-30 13:45:17.16 UTC 286a69c3-6302-4d1c-a787-278fad080727 2012-11-12 16:01:05.954 UTC 91948479-872a-477b-b56b-073869d927cb 2013-02-18 14:48:42.299 UTC 401434ba-30e7-4440-8bdf-ed46318b28fa 2012-11-12 17:50:35.946 UTC 50f0cff2-6fd6-4d18-85c5-df126f1e342b 2013-01-30 09:17:38.323 UTC