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_PartitionFinderNameCall_PartitionFinderArgumentConcatenate_two_stringsstring2Concatenate_two_stringsstring1ModelsetGUIGenePartitionModelsetGUIStatCriteriumModelsetGUILinkingBranchMrBayesParserBLMrBayesParserPartDefMrBayesParserPartFinderMrBayesParserMSAphyMrBayesParsernGenMrBayesParsernRunfasta2phyMSAfastaLoggerJobIDLoggerNameLoggerStdErrorJSTWebDav3InputFile_nameJSTWebDav3InputInputBodyJSTWebDav3InputTokenJSTWebDav3Input_2File_nameJSTWebDav3Input_2TokenJSTWebDav3Input_2InputBodyMerge_String_List_to_a_StringstringlistPathPartitionFinderOuputMrBayesInputLog
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.InvokeAddLinestring1AddLinestring2AddLine_2string1AddLine_2string2AddLine_2_2string1AddLine_2_2string2Split_string_into_string_list_by_regular_expression_2_2_2regexSplit_string_into_string_list_by_regular_expression_2_2_2stringAddLine_2_2_2string1AddLine_2_2_2string2Concatenate_two_stringsstring1Concatenate_two_stringsstring2Concatenate_two_strings_2string1Concatenate_two_strings_2string2Concatenate_two_strings_2_2string1Concatenate_two_strings_2_2string2Flatten_ListinputlistMerge_String_List_to_a_StringstringlistMerge_String_List_to_a_StringseperatorTestPartitionDefBL
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