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changeset 10:2318841ec191 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 821e0f3e4546bc55e093ab63bd9f9b57f2bf772d
author iuc
date Thu, 18 Aug 2022 13:57:26 +0000
parents e6009f23582c
children 91cf1290ba6f
files test-data/relax-in1.fa test-data/relax-in1.nhx test-data/relax-in2.nex test-data/relax-in2.nhx test-data/relax-out2-1.json
diffstat 5 files changed, 142 insertions(+), 214 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/relax-in1.fa	Wed Mar 30 00:18:10 2022 +0000
+++ b/test-data/relax-in1.fa	Thu Aug 18 13:57:26 2022 +0000
@@ -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
--- a/test-data/relax-in1.nhx	Wed Mar 30 00:18:10 2022 +0000
+++ b/test-data/relax-in1.nhx	Thu Aug 18 13:57:26 2022 +0000
@@ -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)
--- a/test-data/relax-in2.nex	Wed Mar 30 00:18:10 2022 +0000
+++ b/test-data/relax-in2.nex	Thu Aug 18 13:57:26 2022 +0000
@@ -8,7 +8,7 @@
 BEGIN TAXA;
 	DIMENSIONS NTAX = 10;
 	TAXLABELS
-		'Human' 'Chimp' 'Baboon' 'RhMonkey' 'Cow' 'Pig' 'Horse' 'Cat' 'Mouse' 'Rat' ;
+		'Baboon' 'Cow' 'Pig' 'Rat' ;
 END;
 
 BEGIN CHARACTERS;
@@ -21,20 +21,14 @@
 	;
 
 MATRIX
-	'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;
 END;
 
 BEGIN TREES;
-	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);
+	TREE tree = (((Pig:0.147969,Cow:0.213430):0.085099,Baboon{PR}:0.003108){PR}:0.340802,Rat:0.050958);
 END;
 
 BEGIN HYPHY;
@@ -42,7 +36,7 @@
 DATA_PANEL_SOURCE_PATH="";
 DataSet CD2 = ReadDataFile (USE_NEXUS_FILE_DATA);
 DataSetFilter CD2_part = CreateFilter (CD2,3,"0-560","(null)","TAA,TAG,TGA");
-Tree CD2_tree=((((Pig,Cow)Node3,Horse,Cat)Node2,((RhMonkey,Baboon)Node9,(Human,Chimp)Node12)Node8)Node1,Rat,Mouse);
+Tree CD2_tree=(((Pig,Cow)Node2,Baboon)Node1,Rat);
 OpenDataPanel(CD2,"(null)","0,0,0,0,2,0,10","MG94xREV_3x4,6,0,14443523,CD2_tree",CD2_LF);
 
 global CD2_part_Shared_AC=0.5710714109234631;
@@ -50,36 +44,16 @@
 global CD2_part_Shared_CG=0.4456308760366715;
 global CD2_part_Shared_CT=0.9454291760502562;
 global CD2_part_Shared_GT=0.3224080259059006;
-CD2_tree.Node12.synRate=0.08168540352543764;
-CD2_tree.Node8.nonSynRate=0.2938890030949185;
-CD2_tree.Human.synRate=1e-30;
 CD2_tree.Baboon.nonSynRate=0;
 CD2_tree.Baboon.synRate=0.01716650886630832;
-CD2_tree.Node12.nonSynRate=0.02962786133931161;
-CD2_tree.Chimp.synRate=1e-30;
-CD2_tree.Chimp.nonSynRate=0.005834136861061837;
-CD2_tree.Node9.nonSynRate=0.0433794394076959;
-CD2_tree.Human.nonSynRate=0;
-CD2_tree.Node9.synRate=0.1139808847086709;
-CD2_tree.Node8.synRate=0.1586154947684889;
 CD2_tree.Rat.synRate=0.1533251749656354;
-CD2_tree.Mouse.nonSynRate=0.2332402459120736;
-CD2_tree.Mouse.synRate=0.4604267094040578;
 CD2_tree.Rat.nonSynRate=0.1585006932449144;
 CD2_tree.Node1.nonSynRate=0.5097883291072822;
 CD2_tree.Node1.synRate=1.227004762734591;
-CD2_tree.RhMonkey.synRate=0;
-CD2_tree.Node3.synRate=0.1877287558837553;
 CD2_tree.Pig.nonSynRate=0.4826366809736332;
-CD2_tree.Horse.nonSynRate=0.518627673056701;
 CD2_tree.Cow.nonSynRate=0.681831503936737;
-CD2_tree.Cat.synRate=0.4672127128189641;
-CD2_tree.Node3.nonSynRate=0.2648957141533021;
-CD2_tree.Horse.synRate=0.430860769501357;
 CD2_tree.Pig.synRate=0.3721230153643161;
 CD2_tree.Node2.synRate=0.2137858662796737;
-CD2_tree.RhMonkey.nonSynRate=0.01161863878954486;
-CD2_tree.Cat.nonSynRate=0.7203773170684773;
 CD2_tree.Node2.nonSynRate=0.1379570235930709;
 CD2_tree.Cow.synRate=0.3646221318370894;
 
--- a/test-data/relax-in2.nhx	Wed Mar 30 00:18:10 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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)
--- a/test-data/relax-out2-1.json	Wed Mar 30 00:18:10 2022 +0000
+++ b/test-data/relax-out2-1.json	Thu Aug 18 13:57:26 2022 +0000
@@ -1,60 +1,55 @@
 {
- "Synonymous site-posteriors":  [
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-  ],
  "analysis":0,
  "branch attributes":{
    "0":{
      "BABOON":{
-       "General descriptive":0.001859562666773025,
+       "General descriptive":0.001858528201768933,
        "MG94xREV with separate rates for branch sets":0.001729040005725717,
        "Nucleotide GTR":0.001685167654714891,
-       "RELAX alternative":0.001434762988174167,
-       "RELAX null":0.001618077326700096,
-       "RELAX partitioned descriptive":0.001426437398554912,
-       "k (general descriptive)":0.09975760133237818,
+       "RELAX alternative":0.001823573976182991,
+       "RELAX null":0.001855504238020734,
+       "RELAX partitioned descriptive":0.001856473113608415,
+       "k (general descriptive)":0.09974837182960776,
        "original name":"BABOON"
       },
      "CAT":{
-       "General descriptive":0.3649705108927348,
+       "General descriptive":0.3649687317465272,
        "MG94xREV with separate rates for branch sets":0.2761191158060541,
        "Nucleotide GTR":0.2660536011315811,
-       "RELAX alternative":0.3757111787573828,
-       "RELAX null":0.360767755751942,
-       "RELAX partitioned descriptive":0.3768226672635935,
-       "k (general descriptive)":2.322824217601444,
+       "RELAX alternative":0.3317928646169214,
+       "RELAX null":0.3252639231399129,
+       "RELAX partitioned descriptive":0.3330192884009499,
+       "k (general descriptive)":2.321295373553348,
        "original name":"CAT"
       },
      "CHIMP":{
-       "General descriptive":0.001848544328521468,
+       "General descriptive":0.00184909269599246,
        "MG94xREV with separate rates for branch sets":0.001822551054713939,
        "Nucleotide GTR":0.001820258053351119,
-       "RELAX alternative":0.001854643673065862,
-       "RELAX null":0.00185572990722179,
-       "RELAX partitioned descriptive":0.001854201499317722,
-       "k (general descriptive)":5.263917013225917,
+       "RELAX alternative":0.00182628703877269,
+       "RELAX null":0.001834608540291232,
+       "RELAX partitioned descriptive":0.001827445389436029,
+       "k (general descriptive)":5.301733626197528,
        "original name":"CHIMP"
       },
      "COW":{
-       "General descriptive":0.3734992963367884,
+       "General descriptive":0.3735020294731436,
        "MG94xREV with separate rates for branch sets":0.248802707042435,
        "Nucleotide GTR":0.2480198736772598,
-       "RELAX alternative":0.3379561449590825,
-       "RELAX null":0.3268684624461423,
-       "RELAX partitioned descriptive":0.336296078659758,
-       "k (general descriptive)":2.847745204182733,
+       "RELAX alternative":0.3080684096213485,
+       "RELAX null":0.2951198100127046,
+       "RELAX partitioned descriptive":0.3113651933641743,
+       "k (general descriptive)":2.848124116654745,
        "original name":"COW"
       },
      "HORSE":{
-       "General descriptive":0.2805104186424681,
+       "General descriptive":0.2803565521817367,
        "MG94xREV with separate rates for branch sets":0.2114983058912022,
        "Nucleotide GTR":0.2090998951755368,
-       "RELAX alternative":0.2639982922145814,
-       "RELAX null":0.2570519477156736,
-       "RELAX partitioned descriptive":0.26200095593742,
-       "k (general descriptive)":1.930891329212253,
+       "RELAX alternative":0.2669775401023034,
+       "RELAX null":0.2560153217844985,
+       "RELAX partitioned descriptive":0.2711533659241344,
+       "k (general descriptive)":1.929084551844662,
        "original name":"HORSE"
       },
      "HUMAN":{
@@ -64,101 +59,101 @@
        "RELAX alternative":0,
        "RELAX null":0,
        "RELAX partitioned descriptive":0,
-       "k (general descriptive)":1.416548546052124,
+       "k (general descriptive)":1.417418953564817,
        "original name":"HUMAN"
       },
      "MOUSE":{
-       "General descriptive":0.1308803878257961,
+       "General descriptive":0.1308909653091745,
        "MG94xREV with separate rates for branch sets":0.1192893635530923,
        "Nucleotide GTR":0.1181058300538561,
-       "RELAX alternative":0.1516183081271659,
-       "RELAX null":0.1483567973872321,
-       "RELAX partitioned descriptive":0.1488950288407203,
-       "k (general descriptive)":0.4621316779775653,
+       "RELAX alternative":0.15085996133762,
+       "RELAX null":0.1469017908982058,
+       "RELAX partitioned descriptive":0.1491287772297175,
+       "k (general descriptive)":0.4628338932722805,
        "original name":"MOUSE"
       },
      "Node1":{
-       "General descriptive":0.3501143091462658,
+       "General descriptive":0.3501950875747647,
        "MG94xREV with separate rates for branch sets":0.2891531817656844,
        "Nucleotide GTR":0.2767105173979571,
-       "RELAX alternative":0.420525835142383,
-       "RELAX null":0.4545405634998693,
-       "RELAX partitioned descriptive":0.4297776151561553,
-       "k (general descriptive)":0.4575702395890889
+       "RELAX alternative":0.3644026907015058,
+       "RELAX null":0.4527247199492397,
+       "RELAX partitioned descriptive":0.4226204412177209,
+       "k (general descriptive)":0.4559088158670693
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      "Node12":{
-       "General descriptive":0.01766178787800134,
+       "General descriptive":0.01767952779767795,
        "MG94xREV with separate rates for branch sets":0.0175770110347634,
        "Nucleotide GTR":0.01784222107494562,
-       "RELAX alternative":0.01626048141633729,
-       "RELAX null":0.01716868534229337,
-       "RELAX partitioned descriptive":0.01647240042293572,
-       "k (general descriptive)":0.124120594408151
+       "RELAX alternative":0.0176558660351027,
+       "RELAX null":0.01825591179366154,
+       "RELAX partitioned descriptive":0.01814639835827904,
+       "k (general descriptive)":0.1240838029653794
       },
      "Node2":{
-       "General descriptive":0.05770266360624338,
+       "General descriptive":0.05770620828101171,
        "MG94xREV with separate rates for branch sets":0.06229443926236622,
        "Nucleotide GTR":0.06614755778044307,
-       "RELAX alternative":0.06487498265124983,
-       "RELAX null":0.06743647945583151,
-       "RELAX partitioned descriptive":0.06330449773182804,
-       "k (general descriptive)":0.5360768532731082
+       "RELAX alternative":0.05866256113025137,
+       "RELAX null":0.06147496751530821,
+       "RELAX partitioned descriptive":0.05724188758009503,
+       "k (general descriptive)":0.5371848217199983
       },
      "Node3":{
-       "General descriptive":0.1330256319960288,
+       "General descriptive":0.1330354609631224,
        "MG94xREV with separate rates for branch sets":0.1003154990002797,
        "Nucleotide GTR":0.09883748387954429,
-       "RELAX alternative":0.1378173139909468,
-       "RELAX null":0.1387701954254672,
-       "RELAX partitioned descriptive":0.136719474302551,
-       "k (general descriptive)":1.981625732305646
+       "RELAX alternative":0.1265135269643693,
+       "RELAX null":0.1276253046950155,
+       "RELAX partitioned descriptive":0.1271876163104063,
+       "k (general descriptive)":1.981364628056296
       },
      "Node8":{
-       "General descriptive":0.1404338383825282,
+       "General descriptive":0.140369727816558,
        "MG94xREV with separate rates for branch sets":0.1127066220459272,
        "Nucleotide GTR":0.1062201244057951,
-       "RELAX alternative":0.1439313895033506,
-       "RELAX null":0.14318831284655,
-       "RELAX partitioned descriptive":0.1481785335086442,
-       "k (general descriptive)":2.211998835217187
+       "RELAX alternative":0.1280322211601967,
+       "RELAX null":0.1343412714385626,
+       "RELAX partitioned descriptive":0.1406663540457613,
+       "k (general descriptive)":2.211767324109487
       },
      "Node9":{
-       "General descriptive":0.02665501999328081,
+       "General descriptive":0.02663291940160552,
        "MG94xREV with separate rates for branch sets":0.02627402966233569,
        "Nucleotide GTR":0.02567813733543303,
-       "RELAX alternative":0.02985671529404269,
-       "RELAX null":0.02953553824738531,
-       "RELAX partitioned descriptive":0.02996950192160838,
-       "k (general descriptive)":0.07343805012797726
+       "RELAX alternative":0.02720907734174326,
+       "RELAX null":0.02752483699250281,
+       "RELAX partitioned descriptive":0.02810928828288993,
+       "k (general descriptive)":0.07329530197274074
       },
      "PIG":{
-       "General descriptive":0.2105401970679286,
+       "General descriptive":0.2104965149960229,
        "MG94xREV with separate rates for branch sets":0.1921302603267553,
        "Nucleotide GTR":0.1871390433004313,
-       "RELAX alternative":0.2517917117490165,
-       "RELAX null":0.2483169436500481,
-       "RELAX partitioned descriptive":0.2506475053874151,
-       "k (general descriptive)":1.582105640200874,
+       "RELAX alternative":0.2174541263946326,
+       "RELAX null":0.2166570805170097,
+       "RELAX partitioned descriptive":0.2198382730708073,
+       "k (general descriptive)":1.581624239713873,
        "original name":"PIG"
       },
      "RAT":{
-       "General descriptive":0.07158272879959397,
+       "General descriptive":0.07156643194841542,
        "MG94xREV with separate rates for branch sets":0.06831927364558048,
        "Nucleotide GTR":0.06661490534189227,
-       "RELAX alternative":0.07311180317129368,
-       "RELAX null":0.07112698282214641,
-       "RELAX partitioned descriptive":0.07451416024404128,
-       "k (general descriptive)":1.317928928374736,
+       "RELAX alternative":0.07273892007491474,
+       "RELAX null":0.07342001791171293,
+       "RELAX partitioned descriptive":0.07588524426470618,
+       "k (general descriptive)":1.318666444029934,
        "original name":"RAT"
       },
      "RHMONKEY":{
-       "General descriptive":0.003673715052669516,
+       "General descriptive":0.003670942377703963,
        "MG94xREV with separate rates for branch sets":0.003755247927570558,
        "Nucleotide GTR":0.003778804730491441,
-       "RELAX alternative":0.004176749981889291,
-       "RELAX null":0.00397871921631754,
-       "RELAX partitioned descriptive":0.004188079354984015,
-       "k (general descriptive)":5.301456309232226,
+       "RELAX alternative":0.003673289414323487,
+       "RELAX null":0.003666197747079884,
+       "RELAX partitioned descriptive":0.003661285250492945,
+       "k (general descriptive)":5.244027200799457,
        "original name":"RHMONKEY"
       }
     },
@@ -207,21 +202,21 @@
   },
  "fits":{
    "General descriptive":{
-     "AIC-c":6945.886057024934,
-     "Log Likelihood":-3420.484282637879,
+     "AIC-c":6945.887251511141,
+     "Log Likelihood":-3420.484879880983,
      "Rate Distributions":{
        "Shared":{
          "0":{
-           "omega":2.201373594751134e-18,
-           "proportion":0.5258178735075876
+           "omega":2.201644423775106e-18,
+           "proportion":0.1667516969215508
           },
          "1":{
-           "omega":2.201373594751134e-18,
-           "proportion":0.01992025780064184
+           "omega":2.201644423775106e-18,
+           "proportion":0.3790423141178453
           },
          "2":{
-           "omega":2.201373412388544,
-           "proportion":0.4542618686917706
+           "omega":2.201644241390081,
+           "proportion":0.4542059889606039
           }
         }
       },
@@ -326,144 +321,116 @@
      "estimated parameters":24
     },
    "RELAX alternative":{
-     "AIC-c":6909.668413948684,
-     "Log Likelihood":-3408.69933855329,
+     "AIC-c":6938.419285358699,
+     "Log Likelihood":-3432.482965101608,
      "Rate Distributions":{
        "Reference":{
          "0":{
            "omega":0,
-           "proportion":0.3825895192221547
+           "proportion":0.2968543549269862
           },
          "1":{
-           "omega":0.003503464580598538,
-           "proportion":0
+           "omega":0,
+           "proportion":0.2447083724876047
           },
          "2":{
-           "omega":2.417572962231385,
-           "proportion":0.6174104807778453
-          }
-        },
-       "Synonymous site-to-site rates":{
-         "0":{
-           "proportion":0.2789425737851868,
-           "rate":0.2834765074731829
-          },
-         "1":{
-           "proportion":0.6311785441975573,
-           "rate":0.9970973177052372
-          },
-         "2":{
-           "proportion":0.089878882017256,
-           "rate":3.244142488658602
+           "omega":3.910413867333085,
+           "proportion":0.4584372725854091
           }
         },
        "Test":{
          "0":{
            "omega":0,
-           "proportion":0.3825895192221547
+           "proportion":0.2968543549269862
           },
          "1":{
-           "omega":0.9998114377116485,
-           "proportion":0
+           "omega":0,
+           "proportion":0.2447083724876047
           },
          "2":{
-           "omega":1.000029443594731,
-           "proportion":0.6174104807778453
+           "omega":1.655264242043239,
+           "proportion":0.4584372725854091
           }
         }
       },
      "display order":2,
-     "estimated parameters":45
+     "estimated parameters":36
     },
    "RELAX null":{
-     "AIC-c":6919.152853316747,
-     "Log Likelihood":-3414.491495151524,
+     "AIC-c":6946.046147526199,
+     "Log Likelihood":-3437.336050862336,
      "Rate Distributions":{
        "Reference":{
          "0":{
-           "omega":0,
-           "proportion":0.3885051761591228
+           "omega":0.07516343499603452,
+           "proportion":0.2524283429126023
           },
          "1":{
-           "omega":0.9958737025997172,
-           "proportion":0
+           "omega":0.1730729265669467,
+           "proportion":0.3734402861071174
           },
          "2":{
-           "omega":1.887643080900262,
-           "proportion":0.6114948238408772
-          }
-        },
-       "Synonymous site-to-site rates":{
-         "0":{
-           "proportion":0.2642938080646302,
-           "rate":0.2741590488311177
-          },
-         "1":{
-           "proportion":0.633162055223991,
-           "rate":0.9728788992663913
-          },
-         "2":{
-           "proportion":0.1025441367113787,
-           "rate":3.038218152856258
+           "omega":3.70326279512502,
+           "proportion":0.3741313709802804
           }
         },
        "Test":{
          "0":{
-           "omega":0,
-           "proportion":0.3885051761591228
+           "omega":0.07516343499603452,
+           "proportion":0.2524283429126023
           },
          "1":{
-           "omega":0.9958737025997172,
-           "proportion":0
+           "omega":0.1730729265669467,
+           "proportion":0.3734402861071174
           },
          "2":{
-           "omega":1.887643080900262,
-           "proportion":0.6114948238408772
+           "omega":3.70326279512502,
+           "proportion":0.3741313709802804
           }
         }
       },
      "display order":3,
-     "estimated parameters":44
+     "estimated parameters":35
     },
    "RELAX partitioned descriptive":{
-     "AIC-c":6917.810941882631,
-     "Log Likelihood":-3408.559317095162,
+     "AIC-c":6944.507313452719,
+     "Log Likelihood":-3431.356991882183,
      "Rate Distributions":{
        "Reference":{
          "0":{
-           "omega":0.03550460650841439,
-           "proportion":0.354985198548996
+           "omega":0,
+           "proportion":0.3694476627871225
           },
          "1":{
-           "omega":0.05439939847728128,
-           "proportion":0.02231130867735708
+           "omega":0.03660893085044142,
+           "proportion":0.1726741298596992
           },
          "2":{
-           "omega":2.333762420535514,
-           "proportion":0.6227034927736469
+           "omega":3.988980749944551,
+           "proportion":0.4578782073531784
           }
         },
        "Test":{
          "0":{
-           "omega":0,
-           "proportion":0.3705590531463396
+           "omega":0.224878249826745,
+           "proportion":0.2953732524277409
           },
          "1":{
-           "omega":0,
-           "proportion":0.06265340406614885
+           "omega":0.231175241198686,
+           "proportion":0.5325206774143161
           },
          "2":{
-           "omega":1.08372848194659,
-           "proportion":0.5667875427875115
+           "omega":4.178788461910403,
+           "proportion":0.172106070157943
           }
         }
       },
      "display order":5,
-     "estimated parameters":49
+     "estimated parameters":40
     }
   },
  "input":{
-   "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/5/working/./input.nex",
+   "file name":"/tmp/tmps1cqwvdh/job_working_directory/000/5/working/./input.nex",
    "number of sequences":10,
    "number of sites":187,
    "partition count":1,
@@ -471,11 +438,11 @@
      "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)"
     }
   },
- "runtime":"2.5.32",
+ "runtime":"2.5.36",
  "test results":{
-   "LRT":11.58431319646934,
-   "p-value":0.0006651049394417186,
-   "relaxation or intensification parameter":3.335337302186161e-05
+   "LRT":9.706171521456781,
+   "p-value":0.001836502097725456,
+   "relaxation or intensification parameter":0.3695692925647034
   },
  "tested":{
    "0":{
@@ -500,27 +467,27 @@
  "timers":{
    "General descriptive model fitting":{
      "order":2,
-     "timer":105
+     "timer":159
     },
    "Overall":{
      "order":0,
-     "timer":3013
+     "timer":428
     },
    "Preliminary model fitting":{
      "order":1,
-     "timer":8
+     "timer":13
     },
    "RELAX alternative model fitting":{
      "order":3,
-     "timer":1229
+     "timer":61
     },
    "RELAX null model fitting":{
      "order":4,
-     "timer":690
+     "timer":53
     },
    "RELAX partitioned descriptive":{
      "order":5,
-     "timer":980
+     "timer":141
     }
   }
 }
\ No newline at end of file