| Previous changeset 32:00b4cf477625 (2022-03-30) Next changeset 34:a809f93e7e6d (2023-03-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 821e0f3e4546bc55e093ab63bd9f9b57f2bf772d |
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modified:
test-data/relax-in1.fa test-data/relax-in1.nhx test-data/relax-in2.nex test-data/relax-out2-1.json |
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removed:
test-data/relax-in2.nhx |
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| diff -r 00b4cf477625 -r d52a803b2b5c test-data/relax-in1.fa --- a/test-data/relax-in1.fa Wed Mar 30 00:22:46 2022 +0000 +++ b/test-data/relax-in1.fa Thu Aug 18 13:54:30 2022 +0000 |
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| @@ -1,20 +1,8 @@ ->Human -AAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC ->Chimp -GAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC >Baboon AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC ->RhMonkey -AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAGATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAAYTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGRCCCCGAATTAAACCTGTATCAAGATGGGAAACATGTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC >Cow ------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACT---CTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT >Pig ---------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGAT---CTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT ->Horse -------------AAGAATATCACCATCTTGGGTGCCCTGGAACGTGATATCAACCTGGACATTCCTGCTTTTCAAATGAGTGAGCATGTAGAAGATATACAATGGAGCAAA------GGAAAAACCAAGATTGCAAAATTCAAAAATGGCAGTATGACTTTCCAGAAAGATAAAACATACGAGGTATTAAAAAATGGAACTCTGAAAATTAAACAT---CTGGAGAGAATTCATGAAGGTACCTACAAGGTAGACGCATATGATAGTGATGGAAAAAATGTGTTGGAGGAAACATTTCATTTGAGCCTTCTAGAGATGGTCTCAAAACCTAATATCTCCTGGAGCTGCACCAACACCACCCTGACCTGCGAGGTGACAAAAGGAACTGACTTTGAGTTAAAACTCTATCTAAATGGGAGAATGATCCAAAAAAGTCCTCGCAAAGTCATCGTATACAAGCGGGCCAGCAACCAAATTGCGTCCTTCAAGTGCACAGCCAATAACACAGTCAGCGAGGAAAGCAGCTCTGTGGTCATCAGGTGTACAGAGAAAGGTCTGGAT ->Cat ----------GCAAATGATGATATCGTCTGGGGTACCCTGGGTCAGGACATCAACCTGGACATTCCTGATTCTCAA---GGGATTAATATAGATGATATACACTGGGAAAAA------GGCAAGAAGAAGGTGGCGAGGTTCCAAATTAGCAACAAGCCTAAGAATCCAGATGAAAAATATAATGTGTCAATGAATGGAACTCTGAAAATTAAACAT---CTGATGCTAGAAGACTGCGATACCTACAAGGTTGTTATATACGATAAGGATGGAAAGAATGTGTTGGATAAAACATTTCAGCTGAAGATTCAAGAGAAGGTCTCAACGCCTAACATCGACTGGAATTGTATCAACAAAACCCTGGTCTGTAAGGTATCAAATGGAACAGACCCTGAATTAAAACTGTACGTAAATGGGACCAGTATCAAGCCCGTTTCTTCGAAGTTCAGCACATACAGGTTTATAAACAAGCAGAAGATATTAGTCAACTGCACGGCAGAAAACAAAGTCAGCAAGGAAAGCGACGTGAAGATGATCACTTGTTCAGAGAAGGGTCTGGAC ->Mouse ----------AGAGACAATGAGACCATCTGGGGTGTCTTGGGTCATGGCATCACCCTGAACATCCCCAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGTAAGG------AGGGGCACCCTGGTCGCAGAGTTTAAAAGGAAGAAGCCACCTTTTTTGATATCAGAAACGTATGAGGTCTTAGCAAACGGATCCCTGAAGATAAAGAAGCCGATGATGAGAAACGACAGTGGCACCTATAATGTAATGGTGTATGGCACAAATGGGATGACTAGGCTGGAGAAGGACCTGGACGTGAGGATTCTGGAGAGGGTCTCAAAGCCCATGATCCACTGGGAATGCCCCAACACAACCCTGACCTGTGCGGTCTTGCAAGGGACAGATTTTGAACTGAAGCTGTATCAAGGGGAAACACTACTCAATAGTCTCCCCCAGAAGAACATGAGTTACCAGTGG---ACCAACCTGAACGCACCATTCAAGTGTGAGGCGATAAACCCGGTCAGCAAGGAGTCTAAGATGGAAGTTGTTAACTGTCCAGAGAAAGGTCTGTCC >Rat ---------AGAGACAGTGGGACCGTCTGGGGTGCCCTGGGTCATGGCATCAACCTGAACATCCCTAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGAGAGG------GGGAGCACCCTGGTTGCCGAGTTTAAAAGGAAGATGAAGCCTTTTTTGAAATCGGGAGCATTTGAGATCTTAGCAAATGGAGACTTGAAGATAAAGAAT---CTGACAAGAGATGACAGTGGCACCTATAATGTAACGGTATACAGCACAAATGGGACACGTATCCTGGACAAGGCACTGGACTTGAGGATTCTAGAGATGGTCTCAAAGCCGATGATCTACTGGGAGTGCAGCAACGCAACCCTGACCTGTGAGGTCTTGGAAGGAACAGATGTTGAACTAAAGCTGTACCAAGGAAAGGAGCATCTCAGGAGCCTCCGTCAGAAGACCATGAGTTACCAGTGG---ACCAACCTGAGAGCACCGTTTAAGTGCAAGGCGGTAAACAGGGTCAGCCAGGAGTCTGAGATGGAAGTTGTCAACTGTCCAGAGAAAGGTCTGCCC |
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| diff -r 00b4cf477625 -r d52a803b2b5c test-data/relax-in1.nhx --- a/test-data/relax-in1.nhx Wed Mar 30 00:22:46 2022 +0000 +++ b/test-data/relax-in1.nhx Thu Aug 18 13:54:30 2022 +0000 |
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| @@ -1,1 +1,1 @@ -((((Pig:0.147969,Cow{TEST}:0.21343):0.085099,Horse{TEST}:0.165787,Cat{TEST}:0.264806):0.058611,((RhMonkey:0.002015,Baboon:0.003108):0.022733,(Human:0.004349,Chimp:0.000799):0.011873):0.101856):0.340802,Rat:0.050958,Mouse:0.09795) \ No newline at end of file +(((Pig:0.147969,Cow{TEST}:0.21343):0.085099,Baboon:0.011873):0.340802,Rat:0.050958) |
| b |
| diff -r 00b4cf477625 -r d52a803b2b5c test-data/relax-in2.nex --- a/test-data/relax-in2.nex Wed Mar 30 00:22:46 2022 +0000 +++ b/test-data/relax-in2.nex Thu Aug 18 13:54:30 2022 +0000 |
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| b"@@ -8,7 +8,7 @@\n BEGIN TAXA;\n \tDIMENSIONS NTAX = 10;\n \tTAXLABELS\n-\t\t'Human' 'Chimp' 'Baboon' 'RhMonkey' 'Cow' 'Pig' 'Horse' 'Cat' 'Mouse' 'Rat' ;\n+\t\t'Baboon' 'Cow' 'Pig' 'Rat' ;\n END;\n \n BEGIN CHARACTERS;\n@@ -21,20 +21,14 @@\n \t;\n \n MATRIX\n-\t'Human' AAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n-\t'Chimp' GAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n \t'Baboon' AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n-\t'RhMonkey' AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAGATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAAYTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGRCCCCGAATTAAACCTGTATCAAGATGGGAAACATGTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n \t'Cow' ------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACT---CTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT\n \t'Pig' ---------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGAT---CTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT\n-\t'Horse' ------------AAGAATATCACCATCTTGGGTGCCCTGGAACGTGATATCAACCTGGACATTCCTGCTTTTCAAATGAGTGAGCATGTAGAAGATATACAATGGAGCAAA------GGAAAAACCAAGATTGCAAAATTCAAAAATGGCAGTATGACTTTCCAGAAAGATAAAACATACGAGGTATTAAAAAATGGAACTCTGAAAATTAAACAT---CTGGAGAGAATTCATGAAGGTACCTACAAGGTAGACGCATATGATAGTGATGGAAAAAATGTGTTGGAGGA"..b'TTAGCAACAAGCCTAAGAATCCAGATGAAAAATATAATGTGTCAATGAATGGAACTCTGAAAATTAAACAT---CTGATGCTAGAAGACTGCGATACCTACAAGGTTGTTATATACGATAAGGATGGAAAGAATGTGTTGGATAAAACATTTCAGCTGAAGATTCAAGAGAAGGTCTCAACGCCTAACATCGACTGGAATTGTATCAACAAAACCCTGGTCTGTAAGGTATCAAATGGAACAGACCCTGAATTAAAACTGTACGTAAATGGGACCAGTATCAAGCCCGTTTCTTCGAAGTTCAGCACATACAGGTTTATAAACAAGCAGAAGATATTAGTCAACTGCACGGCAGAAAACAAAGTCAGCAAGGAAAGCGACGTGAAGATGATCACTTGTTCAGAGAAGGGTCTGGAC\n-\t\'Mouse\' ---------AGAGACAATGAGACCATCTGGGGTGTCTTGGGTCATGGCATCACCCTGAACATCCCCAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGTAAGG------AGGGGCACCCTGGTCGCAGAGTTTAAAAGGAAGAAGCCACCTTTTTTGATATCAGAAACGTATGAGGTCTTAGCAAACGGATCCCTGAAGATAAAGAAGCCGATGATGAGAAACGACAGTGGCACCTATAATGTAATGGTGTATGGCACAAATGGGATGACTAGGCTGGAGAAGGACCTGGACGTGAGGATTCTGGAGAGGGTCTCAAAGCCCATGATCCACTGGGAATGCCCCAACACAACCCTGACCTGTGCGGTCTTGCAAGGGACAGATTTTGAACTGAAGCTGTATCAAGGGGAAACACTACTCAATAGTCTCCCCCAGAAGAACATGAGTTACCAGTGG---ACCAACCTGAACGCACCATTCAAGTGTGAGGCGATAAACCCGGTCAGCAAGGAGTCTAAGATGGAAGTTGTTAACTGTCCAGAGAAAGGTCTGTCC\n \t\'Rat\' ---------AGAGACAGTGGGACCGTCTGGGGTGCCCTGGGTCATGGCATCAACCTGAACATCCCTAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGAGAGG------GGGAGCACCCTGGTTGCCGAGTTTAAAAGGAAGATGAAGCCTTTTTTGAAATCGGGAGCATTTGAGATCTTAGCAAATGGAGACTTGAAGATAAAGAAT---CTGACAAGAGATGACAGTGGCACCTATAATGTAACGGTATACAGCACAAATGGGACACGTATCCTGGACAAGGCACTGGACTTGAGGATTCTAGAGATGGTCTCAAAGCCGATGATCTACTGGGAGTGCAGCAACGCAACCCTGACCTGTGAGGTCTTGGAAGGAACAGATGTTGAACTAAAGCTGTACCAAGGAAAGGAGCATCTCAGGAGCCTCCGTCAGAAGACCATGAGTTACCAGTGG---ACCAACCTGAGAGCACCGTTTAAGTGCAAGGCGGTAAACAGGGTCAGCCAGGAGTCTGAGATGGAAGTTGTCAACTGTCCAGAGAAAGGTCTGCCC;\n END;\n \n BEGIN TREES;\n-\tTREE tree = ((((Pig:0.147969,Cow:0.213430):0.085099,Horse:0.165787,Cat:0.264806):0.058611,((RhMonkey{PR}:0.002015,Baboon{PR}:0.003108){PR}:0.022733,(Human{PR}:0.004349,Chimp{PR}:0.000799){PR}:0.011873){PR}:0.101856){PR}:0.340802,Rat:0.050958,Mouse:0.097950);\n+\tTREE tree = (((Pig:0.147969,Cow:0.213430):0.085099,Baboon{PR}:0.003108){PR}:0.340802,Rat:0.050958);\n END;\n \n BEGIN HYPHY;\n@@ -42,7 +36,7 @@\n DATA_PANEL_SOURCE_PATH="";\n DataSet CD2 = ReadDataFile (USE_NEXUS_FILE_DATA);\n DataSetFilter CD2_part = CreateFilter (CD2,3,"0-560","(null)","TAA,TAG,TGA");\n-Tree CD2_tree=((((Pig,Cow)Node3,Horse,Cat)Node2,((RhMonkey,Baboon)Node9,(Human,Chimp)Node12)Node8)Node1,Rat,Mouse);\n+Tree CD2_tree=(((Pig,Cow)Node2,Baboon)Node1,Rat);\n OpenDataPanel(CD2,"(null)","0,0,0,0,2,0,10","MG94xREV_3x4,6,0,14443523,CD2_tree",CD2_LF);\n \n global CD2_part_Shared_AC=0.5710714109234631;\n@@ -50,36 +44,16 @@\n global CD2_part_Shared_CG=0.4456308760366715;\n global CD2_part_Shared_CT=0.9454291760502562;\n global CD2_part_Shared_GT=0.3224080259059006;\n-CD2_tree.Node12.synRate=0.08168540352543764;\n-CD2_tree.Node8.nonSynRate=0.2938890030949185;\n-CD2_tree.Human.synRate=1e-30;\n CD2_tree.Baboon.nonSynRate=0;\n CD2_tree.Baboon.synRate=0.01716650886630832;\n-CD2_tree.Node12.nonSynRate=0.02962786133931161;\n-CD2_tree.Chimp.synRate=1e-30;\n-CD2_tree.Chimp.nonSynRate=0.005834136861061837;\n-CD2_tree.Node9.nonSynRate=0.0433794394076959;\n-CD2_tree.Human.nonSynRate=0;\n-CD2_tree.Node9.synRate=0.1139808847086709;\n-CD2_tree.Node8.synRate=0.1586154947684889;\n CD2_tree.Rat.synRate=0.1533251749656354;\n-CD2_tree.Mouse.nonSynRate=0.2332402459120736;\n-CD2_tree.Mouse.synRate=0.4604267094040578;\n CD2_tree.Rat.nonSynRate=0.1585006932449144;\n CD2_tree.Node1.nonSynRate=0.5097883291072822;\n CD2_tree.Node1.synRate=1.227004762734591;\n-CD2_tree.RhMonkey.synRate=0;\n-CD2_tree.Node3.synRate=0.1877287558837553;\n CD2_tree.Pig.nonSynRate=0.4826366809736332;\n-CD2_tree.Horse.nonSynRate=0.518627673056701;\n CD2_tree.Cow.nonSynRate=0.681831503936737;\n-CD2_tree.Cat.synRate=0.4672127128189641;\n-CD2_tree.Node3.nonSynRate=0.2648957141533021;\n-CD2_tree.Horse.synRate=0.430860769501357;\n CD2_tree.Pig.synRate=0.3721230153643161;\n CD2_tree.Node2.synRate=0.2137858662796737;\n-CD2_tree.RhMonkey.nonSynRate=0.01161863878954486;\n-CD2_tree.Cat.nonSynRate=0.7203773170684773;\n CD2_tree.Node2.nonSynRate=0.1379570235930709;\n CD2_tree.Cow.synRate=0.3646221318370894;\n \n' |
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| diff -r 00b4cf477625 -r d52a803b2b5c test-data/relax-in2.nhx --- a/test-data/relax-in2.nhx Wed Mar 30 00:22:46 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -((((Pig{TEST}:0.147969,Cow{TEST}:0.21343){TEST}:0.085099,Horse:0.165787,Cat:0.264806){TEST}:0.058611,((RhMonkey{REFERENCE}:0.002015,Baboon{REFERENCE}:0.003108){REFERENCE}:0.022733,(Human{REFERENCE}:0.004349,Chimp{REFERENCE}:0.000799):0.011873){REFERENCE}:0.101856){REFERENCE}:0.340802,Rat{REFERENCE}:0.050958,Mouse{REFERENCE}:0.09795) |
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| diff -r 00b4cf477625 -r d52a803b2b5c test-data/relax-out2-1.json --- a/test-data/relax-out2-1.json Wed Mar 30 00:22:46 2022 +0000 +++ b/test-data/relax-out2-1.json Thu Aug 18 13:54:30 2022 +0000 |
| [ |
| b'@@ -1,60 +1,55 @@\n {\n- "Synonymous site-posteriors": [\n-[0.6636913410863983, 0.4162861463391083, 0.4207669648198341, 0.5266957556553843, 0.7895328001950979, 0.9272590205679656, 0.6152945530195142, 0.7578515907144813, 0.1238947876214084, 0.3018037085532145, 0.2282864078469784, 0.7937331893941735, 0.5320234040808555, 0.4706871966418729, 0.5439405260809865, 0.1517881809649885, 0.09043162428247122, 0.08685065723885507, 0.03885767834229433, 0.05375215759679093, 0.1268225432845697, 0.07577668231270167, 0.6052751007842404, 0.2502160552371602, 0.2736708121460947, 0.7706988555442902, 0.748841088623575, 0.5723843790763415, 0.8949826459565234, 0.6384606763319275, 0.8239292808797724, 0.1664437117300734, 0.06847586601224155, 0.8824121911043322, 0.1271766673209644, 0.1148021398435604, 0.4117122840037579, 0.406499277480147, 0.4008888256405372, 0.8646423634969567, 0.8190691829853963, 0.500042208706628, 0.06797606990283254, 0.8587865476515109, 0.2593957205794197, 0.9238491908671513, 0.8512119846143551, 0.3063762561200102, 0.6669337037749883, 0.8301646821437867, 0.636853262388444, 0.2905505446517289, 0.241935494101366, 0.8128255914518664, 0.8694325465217606, 0.848675874090462, 0.7267309584033903, 0.6911098971620047, 0.583052312866751, 0.7867301296752277, 0.8804662810822645, 0.809644890871663, 0.3376753254168838, 0.8283707254597538, 0.4508845830660299, 0.0216331593168105, 0.3776212213040052, 0.07931015513156162, 0.2950308574589764, 0.1222844084424193, 0.2323128587705404, 0.8289275512891175, 0.631178544197552, 0.05325361766368054, 0.8662251485184755, 0.3212301783117932, 0.861017744903573, 0.5761459249816555, 0.7343170662946317, 0.09741215372980042, 0.1807849329793456, 0.4569927206185401, 0.1643327673634512, 0.1185284443150185, 0.7324030664891016, 0.8472376168908595, 0.8234507825433042, 0.3173650640633187, 0.9292941067446137, 0.2735709551124761, 0.06276324502006964, 0.8863623602779909, 0.8489458938246637, 0.9130985854899469, 0.2797994574222102, 0.9075929417789967, 0.5150137541063844, 0.6723801037322925, 0.06367665954274145, 0.7320704660828672, 0.3527697452184735, 0.8461914351678148, 0.1351211810935134, 0.4613328492603073, 0.124276342334713, 0.8475110259360163, 0.06206865929630392, 0.04122997041189784, 0.8672530362064098, 0.4581644690927911, 0.8415744872053624, 0.1236376392825715, 0.9203127839835408, 0.1271766673209644, 0.8695568439105728, 0.3242726536321666, 0.6064715811235907, 0.1165318836810881, 0.8722046458122451, 0.2149812075751182, 0.0665951965283386, 0.2742588346922531, 0.3653273246144033, 0.721568903142608, 0.2413820620693605, 0.588103471777193, 0.8686043286753734, 0.08010632672074527, 0.5761580378346324, 0.523544810651528, 0.7668186650136124, 0.731052877850959, 0.329467117190821, 0.3208367729701002, 0.06144214634573335, 0.8062919404136638, 0.6220061302015701, 0.2090699504697991, 0.9185889308419551, 0.7767477941019779, 0.5356868588016898, 0.8031407570629746, 0.9042937966352298, 0.7393000429370805, 0.5400823150565389, 0.7357099400943075, 0.9523857813416914, 0.1564516235889077, 0.4882755555291234, 0.1252145971401747, 0.9240797408523314, 0.3440045440887274, 0.2962312024479645, 0.7573666819357475, 0.8253574958581319, 0.1229691454797458, 0.5683960261123714, 0.8313273153092753, 0.8469672878626771, 0.9486952624246412, 0.9172349146810788, 0.3831591722552873, 0.1357178596976572, 0.363473489194153, 0.9082063423261078, 0.7310413241232628, 0.8851632091676694, 0.04945472390779559, 0.7711621490316225, 0.05488172075128287, 0.5228323482367553, 0.9173152634471772, 0.5124114157230398, 0.346256158312588, 0.6630870619405116, 0.9355504393694619, 0.7330631304859381, 0.8707601306551315, 0.7291701265889592, 0.8821257366537769, 0.04095247534309823, 0.557046605833562, 0.2622389511630402, 0.6288683743714585, 0.02357245006214095, 0.01713741578412558, 0.6313826523714624],\n- [0.2743023322221135, 0.5648645480971858, 0.5610960776914764, 0.4621444588317666, 0.1819965032117472, 0.01517197054895779, 0.001285397066934852, 0.237770173435577, 0.8760503299639748, 0.6966768513'..b'92663913\n- },\n- "2":{\n- "proportion":0.1025441367113787,\n- "rate":3.038218152856258\n+ "omega":3.70326279512502,\n+ "proportion":0.3741313709802804\n }\n },\n "Test":{\n "0":{\n- "omega":0,\n- "proportion":0.3885051761591228\n+ "omega":0.07516343499603452,\n+ "proportion":0.2524283429126023\n },\n "1":{\n- "omega":0.9958737025997172,\n- "proportion":0\n+ "omega":0.1730729265669467,\n+ "proportion":0.3734402861071174\n },\n "2":{\n- "omega":1.887643080900262,\n- "proportion":0.6114948238408772\n+ "omega":3.70326279512502,\n+ "proportion":0.3741313709802804\n }\n }\n },\n "display order":3,\n- "estimated parameters":44\n+ "estimated parameters":35\n },\n "RELAX partitioned descriptive":{\n- "AIC-c":6917.810941882631,\n- "Log Likelihood":-3408.559317095162,\n+ "AIC-c":6944.507313452719,\n+ "Log Likelihood":-3431.356991882183,\n "Rate Distributions":{\n "Reference":{\n "0":{\n- "omega":0.03550460650841439,\n- "proportion":0.354985198548996\n+ "omega":0,\n+ "proportion":0.3694476627871225\n },\n "1":{\n- "omega":0.05439939847728128,\n- "proportion":0.02231130867735708\n+ "omega":0.03660893085044142,\n+ "proportion":0.1726741298596992\n },\n "2":{\n- "omega":2.333762420535514,\n- "proportion":0.6227034927736469\n+ "omega":3.988980749944551,\n+ "proportion":0.4578782073531784\n }\n },\n "Test":{\n "0":{\n- "omega":0,\n- "proportion":0.3705590531463396\n+ "omega":0.224878249826745,\n+ "proportion":0.2953732524277409\n },\n "1":{\n- "omega":0,\n- "proportion":0.06265340406614885\n+ "omega":0.231175241198686,\n+ "proportion":0.5325206774143161\n },\n "2":{\n- "omega":1.08372848194659,\n- "proportion":0.5667875427875115\n+ "omega":4.178788461910403,\n+ "proportion":0.172106070157943\n }\n }\n },\n "display order":5,\n- "estimated parameters":49\n+ "estimated parameters":40\n }\n },\n "input":{\n- "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/5/working/./input.nex",\n+ "file name":"/tmp/tmps1cqwvdh/job_working_directory/000/5/working/./input.nex",\n "number of sequences":10,\n "number of sites":187,\n "partition count":1,\n@@ -471,11 +438,11 @@\n "0":"((((PIG:0.147969,COW:0.21343)Node3:0.08509899999999999,HORSE:0.165787,CAT:0.264806)Node2:0.058611,((RHMONKEY:0.002015,BABOON:0.003108)Node9:0.022733,(HUMAN:0.004349,CHIMP:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,RAT:0.050958,MOUSE:0.09795)"\n }\n },\n- "runtime":"2.5.32",\n+ "runtime":"2.5.36",\n "test results":{\n- "LRT":11.58431319646934,\n- "p-value":0.0006651049394417186,\n- "relaxation or intensification parameter":3.335337302186161e-05\n+ "LRT":9.706171521456781,\n+ "p-value":0.001836502097725456,\n+ "relaxation or intensification parameter":0.3695692925647034\n },\n "tested":{\n "0":{\n@@ -500,27 +467,27 @@\n "timers":{\n "General descriptive model fitting":{\n "order":2,\n- "timer":105\n+ "timer":159\n },\n "Overall":{\n "order":0,\n- "timer":3013\n+ "timer":428\n },\n "Preliminary model fitting":{\n "order":1,\n- "timer":8\n+ "timer":13\n },\n "RELAX alternative model fitting":{\n "order":3,\n- "timer":1229\n+ "timer":61\n },\n "RELAX null model fitting":{\n "order":4,\n- "timer":690\n+ "timer":53\n },\n "RELAX partitioned descriptive":{\n "order":5,\n- "timer":980\n+ "timer":141\n }\n }\n }\n\\ No newline at end of file\n' |