Mercurial > repos > iuc > hyphy_fade
comparison test-data/relax-in2.nex @ 25:5e8d0e777033 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
| author | iuc |
|---|---|
| date | Tue, 27 Apr 2021 18:06:34 +0000 |
| parents | |
| children | a73fff151e38 |
comparison
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| 24:64380f4e296a | 25:5e8d0e777033 |
|---|---|
| 1 #NEXUS | |
| 2 | |
| 3 [ | |
| 4 Generated by HYPHY 0.9920070619beta(MP) for MacOS(Carbon) on Thu Jun 21 16:59:04 2007 | |
| 5 | |
| 6 ] | |
| 7 | |
| 8 BEGIN TAXA; | |
| 9 DIMENSIONS NTAX = 10; | |
| 10 TAXLABELS | |
| 11 'Human' 'Chimp' 'Baboon' 'RhMonkey' 'Cow' 'Pig' 'Horse' 'Cat' 'Mouse' 'Rat' ; | |
| 12 END; | |
| 13 | |
| 14 BEGIN CHARACTERS; | |
| 15 DIMENSIONS NCHAR = 561; | |
| 16 FORMAT | |
| 17 DATATYPE = DNA | |
| 18 | |
| 19 GAP=- | |
| 20 MISSING=? | |
| 21 ; | |
| 22 | |
| 23 MATRIX | |
| 24 'Human' AAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC | |
| 25 'Chimp' GAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC | |
| 26 'Baboon' AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC | |
| 27 'RhMonkey' AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAGATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAAYTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGRCCCCGAATTAAACCTGTATCAAGATGGGAAACATGTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC | |
| 28 'Cow' ------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACT---CTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT | |
| 29 'Pig' ---------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGAT---CTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT | |
| 30 'Horse' ------------AAGAATATCACCATCTTGGGTGCCCTGGAACGTGATATCAACCTGGACATTCCTGCTTTTCAAATGAGTGAGCATGTAGAAGATATACAATGGAGCAAA------GGAAAAACCAAGATTGCAAAATTCAAAAATGGCAGTATGACTTTCCAGAAAGATAAAACATACGAGGTATTAAAAAATGGAACTCTGAAAATTAAACAT---CTGGAGAGAATTCATGAAGGTACCTACAAGGTAGACGCATATGATAGTGATGGAAAAAATGTGTTGGAGGAAACATTTCATTTGAGCCTTCTAGAGATGGTCTCAAAACCTAATATCTCCTGGAGCTGCACCAACACCACCCTGACCTGCGAGGTGACAAAAGGAACTGACTTTGAGTTAAAACTCTATCTAAATGGGAGAATGATCCAAAAAAGTCCTCGCAAAGTCATCGTATACAAGCGGGCCAGCAACCAAATTGCGTCCTTCAAGTGCACAGCCAATAACACAGTCAGCGAGGAAAGCAGCTCTGTGGTCATCAGGTGTACAGAGAAAGGTCTGGAT | |
| 31 'Cat' ---------GCAAATGATGATATCGTCTGGGGTACCCTGGGTCAGGACATCAACCTGGACATTCCTGATTCTCAA---GGGATTAATATAGATGATATACACTGGGAAAAA------GGCAAGAAGAAGGTGGCGAGGTTCCAAATTAGCAACAAGCCTAAGAATCCAGATGAAAAATATAATGTGTCAATGAATGGAACTCTGAAAATTAAACAT---CTGATGCTAGAAGACTGCGATACCTACAAGGTTGTTATATACGATAAGGATGGAAAGAATGTGTTGGATAAAACATTTCAGCTGAAGATTCAAGAGAAGGTCTCAACGCCTAACATCGACTGGAATTGTATCAACAAAACCCTGGTCTGTAAGGTATCAAATGGAACAGACCCTGAATTAAAACTGTACGTAAATGGGACCAGTATCAAGCCCGTTTCTTCGAAGTTCAGCACATACAGGTTTATAAACAAGCAGAAGATATTAGTCAACTGCACGGCAGAAAACAAAGTCAGCAAGGAAAGCGACGTGAAGATGATCACTTGTTCAGAGAAGGGTCTGGAC | |
| 32 'Mouse' ---------AGAGACAATGAGACCATCTGGGGTGTCTTGGGTCATGGCATCACCCTGAACATCCCCAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGTAAGG------AGGGGCACCCTGGTCGCAGAGTTTAAAAGGAAGAAGCCACCTTTTTTGATATCAGAAACGTATGAGGTCTTAGCAAACGGATCCCTGAAGATAAAGAAGCCGATGATGAGAAACGACAGTGGCACCTATAATGTAATGGTGTATGGCACAAATGGGATGACTAGGCTGGAGAAGGACCTGGACGTGAGGATTCTGGAGAGGGTCTCAAAGCCCATGATCCACTGGGAATGCCCCAACACAACCCTGACCTGTGCGGTCTTGCAAGGGACAGATTTTGAACTGAAGCTGTATCAAGGGGAAACACTACTCAATAGTCTCCCCCAGAAGAACATGAGTTACCAGTGG---ACCAACCTGAACGCACCATTCAAGTGTGAGGCGATAAACCCGGTCAGCAAGGAGTCTAAGATGGAAGTTGTTAACTGTCCAGAGAAAGGTCTGTCC | |
| 33 'Rat' ---------AGAGACAGTGGGACCGTCTGGGGTGCCCTGGGTCATGGCATCAACCTGAACATCCCTAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGAGAGG------GGGAGCACCCTGGTTGCCGAGTTTAAAAGGAAGATGAAGCCTTTTTTGAAATCGGGAGCATTTGAGATCTTAGCAAATGGAGACTTGAAGATAAAGAAT---CTGACAAGAGATGACAGTGGCACCTATAATGTAACGGTATACAGCACAAATGGGACACGTATCCTGGACAAGGCACTGGACTTGAGGATTCTAGAGATGGTCTCAAAGCCGATGATCTACTGGGAGTGCAGCAACGCAACCCTGACCTGTGAGGTCTTGGAAGGAACAGATGTTGAACTAAAGCTGTACCAAGGAAAGGAGCATCTCAGGAGCCTCCGTCAGAAGACCATGAGTTACCAGTGG---ACCAACCTGAGAGCACCGTTTAAGTGCAAGGCGGTAAACAGGGTCAGCCAGGAGTCTGAGATGGAAGTTGTCAACTGTCCAGAGAAAGGTCTGCCC; | |
| 34 END; | |
| 35 | |
| 36 BEGIN TREES; | |
| 37 TREE 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); | |
| 38 END; | |
| 39 | |
| 40 BEGIN HYPHY; | |
| 41 | |
| 42 DATA_PANEL_SOURCE_PATH=""; | |
| 43 DataSet CD2 = ReadDataFile (USE_NEXUS_FILE_DATA); | |
| 44 DataSetFilter CD2_part = CreateFilter (CD2,3,"0-560","(null)","TAA,TAG,TGA"); | |
| 45 Tree CD2_tree=((((Pig,Cow)Node3,Horse,Cat)Node2,((RhMonkey,Baboon)Node9,(Human,Chimp)Node12)Node8)Node1,Rat,Mouse); | |
| 46 OpenDataPanel(CD2,"(null)","0,0,0,0,2,0,10","MG94xREV_3x4,6,0,14443523,CD2_tree",CD2_LF); | |
| 47 | |
| 48 global CD2_part_Shared_AC=0.5710714109234631; | |
| 49 global CD2_part_Shared_AT=0.2756961373814887; | |
| 50 global CD2_part_Shared_CG=0.4456308760366715; | |
| 51 global CD2_part_Shared_CT=0.9454291760502562; | |
| 52 global CD2_part_Shared_GT=0.3224080259059006; | |
| 53 CD2_tree.Node12.synRate=0.08168540352543764; | |
| 54 CD2_tree.Node8.nonSynRate=0.2938890030949185; | |
| 55 CD2_tree.Human.synRate=1e-30; | |
| 56 CD2_tree.Baboon.nonSynRate=0; | |
| 57 CD2_tree.Baboon.synRate=0.01716650886630832; | |
| 58 CD2_tree.Node12.nonSynRate=0.02962786133931161; | |
| 59 CD2_tree.Chimp.synRate=1e-30; | |
| 60 CD2_tree.Chimp.nonSynRate=0.005834136861061837; | |
| 61 CD2_tree.Node9.nonSynRate=0.0433794394076959; | |
| 62 CD2_tree.Human.nonSynRate=0; | |
| 63 CD2_tree.Node9.synRate=0.1139808847086709; | |
| 64 CD2_tree.Node8.synRate=0.1586154947684889; | |
| 65 CD2_tree.Rat.synRate=0.1533251749656354; | |
| 66 CD2_tree.Mouse.nonSynRate=0.2332402459120736; | |
| 67 CD2_tree.Mouse.synRate=0.4604267094040578; | |
| 68 CD2_tree.Rat.nonSynRate=0.1585006932449144; | |
| 69 CD2_tree.Node1.nonSynRate=0.5097883291072822; | |
| 70 CD2_tree.Node1.synRate=1.227004762734591; | |
| 71 CD2_tree.RhMonkey.synRate=0; | |
| 72 CD2_tree.Node3.synRate=0.1877287558837553; | |
| 73 CD2_tree.Pig.nonSynRate=0.4826366809736332; | |
| 74 CD2_tree.Horse.nonSynRate=0.518627673056701; | |
| 75 CD2_tree.Cow.nonSynRate=0.681831503936737; | |
| 76 CD2_tree.Cat.synRate=0.4672127128189641; | |
| 77 CD2_tree.Node3.nonSynRate=0.2648957141533021; | |
| 78 CD2_tree.Horse.synRate=0.430860769501357; | |
| 79 CD2_tree.Pig.synRate=0.3721230153643161; | |
| 80 CD2_tree.Node2.synRate=0.2137858662796737; | |
| 81 CD2_tree.RhMonkey.nonSynRate=0.01161863878954486; | |
| 82 CD2_tree.Cat.nonSynRate=0.7203773170684773; | |
| 83 CD2_tree.Node2.nonSynRate=0.1379570235930709; | |
| 84 CD2_tree.Cow.synRate=0.3646221318370894; | |
| 85 | |
| 86 END; |