# HG changeset patch
# User iuc
# Date 1770725138 0
# Node ID 8c26d4d128b3e8f2ee51c1072885890439896178
# Parent  ff2724696a7d4565c787a48bbbeffa877d8e7f22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy commit db3cc714a88f1c34dfa888b749a30b17bc898ee9

diff -r ff2724696a7d -r 8c26d4d128b3 macros.xml
--- a/macros.xml	Tue Oct 07 20:39:19 2025 +0000
+++ b/macros.xml	Tue Feb 10 12:05:38 2026 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">2.5.83</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@TOOL_VERSION@">2.5.93</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">24.0</token>
     <token name="@SHELL_OPTIONS@">export TERM="vt100"; </token>
 
diff -r ff2724696a7d -r 8c26d4d128b3 test-data/absrel-in1.fa
--- a/test-data/absrel-in1.fa	Tue Oct 07 20:39:19 2025 +0000
+++ b/test-data/absrel-in1.fa	Tue Feb 10 12:05:38 2026 +0000
@@ -1,8 +1,8 @@
 >Baboon
-AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC
+AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCATCTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC
 >Cow
-------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACT---CTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT
+------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACTCTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT
 >Pig
----------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGAT---CTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT
+---------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGATCTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT
 >Rat
----------AGAGACAGTGGGACCGTCTGGGGTGCCCTGGGTCATGGCATCAACCTGAACATCCCTAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGAGAGG------GGGAGCACCCTGGTTGCCGAGTTTAAAAGGAAGATGAAGCCTTTTTTGAAATCGGGAGCATTTGAGATCTTAGCAAATGGAGACTTGAAGATAAAGAAT---CTGACAAGAGATGACAGTGGCACCTATAATGTAACGGTATACAGCACAAATGGGACACGTATCCTGGACAAGGCACTGGACTTGAGGATTCTAGAGATGGTCTCAAAGCCGATGATCTACTGGGAGTGCAGCAACGCAACCCTGACCTGTGAGGTCTTGGAAGGAACAGATGTTGAACTAAAGCTGTACCAAGGAAAGGAGCATCTCAGGAGCCTCCGTCAGAAGACCATGAGTTACCAGTGG---ACCAACCTGAGAGCACCGTTTAAGTGCAAGGCGGTAAACAGGGTCAGCCAGGAGTCTGAGATGGAAGTTGTCAACTGTCCAGAGAAAGGTCTGCCC
+---------AGAGACAGTGGGACCGTCTGGGGTGCCCTGGGTCATGGCATCAACCTGAACATCCCTAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGAGAGG------GGGAGCACCCTGGTTGCCGAGTTTAAAAGGAAGATGAAGCCTTTTTTGAAATCGGGAGCATTTGAGATCTTAGCAAATGGAGACTTGAAGATAAAGAATCTGACAAGAGATGACAGTGGCACCTATAATGTAACGGTATACAGCACAAATGGGACACGTATCCTGGACAAGGCACTGGACTTGAGGATTCTAGAGATGGTCTCAAAGCCGATGATCTACTGGGAGTGCAGCAACGCAACCCTGACCTGTGAGGTCTTGGAAGGAACAGATGTTGAACTAAAGCTGTACCAAGGAAAGGAGCATCTCAGGAGCCTCCGTCAGAAGACCATGAGTTACCAGTGG---ACCAACCTGAGAGCACCGTTTAAGTGCAAGGCGGTAAACAGGGTCAGCCAGGAGTCTGAGATGGAAGTTGTCAACTGTCCAGAGAAAGGTCTGCCC
diff -r ff2724696a7d -r 8c26d4d128b3 test-data/annotate-out1-full.nhx
--- a/test-data/annotate-out1-full.nhx	Tue Oct 07 20:39:19 2025 +0000
+++ b/test-data/annotate-out1-full.nhx	Tue Feb 10 12:05:38 2026 +0000
@@ -1,1 +1,1 @@
-((gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1:0.000523,epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021{Annotated}:1e-06)Node1:1e-06,REFERENCE:0.000262,(gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4{Annotated}:0.001835,(gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3:1e-06,(gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1{Annotated}:0.000786,(gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1{Annotated}:0.000785,epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021{Annotated}:0.823959)Node11{Annotated}:1e-06)Node9{Annotated}:1e-06)Node7:0.000262)Node5:1e-06)Node5
\ No newline at end of file
+((gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1:0.000523,epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021{Annotated}:1e-06)Node1:1e-06,REFERENCE:0.000262,(gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4{Annotated}:0.001835,(gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3:1e-06,(gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1{Annotated}:0.000786,(gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1{Annotated}:0.000785,epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021{Annotated}:0.823959)Node11{Annotated}:1e-06)Node9{Annotated}:1e-06)Node7:0.000262)Node5:1e-06)
\ No newline at end of file
diff -r ff2724696a7d -r 8c26d4d128b3 test-data/cln-stop-codons.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cln-stop-codons.fa	Tue Feb 10 12:05:38 2026 +0000
@@ -0,0 +1,6 @@
+>GoodSeq
+ATGGCGACC
+>StopSeq
+ATGTAGGCG
+>GoodSeqDup
+ATGGCGACC
\ No newline at end of file
diff -r ff2724696a7d -r 8c26d4d128b3 test-data/relax-in2.nex
--- a/test-data/relax-in2.nex	Tue Oct 07 20:39:19 2025 +0000
+++ b/test-data/relax-in2.nex	Tue Feb 10 12:05:38 2026 +0000
@@ -6,7 +6,7 @@
 ]
 
 BEGIN TAXA;
-	DIMENSIONS NTAX = 10;
+	DIMENSIONS NTAX = 4;
 	TAXLABELS
 		'Baboon' 'Cow' 'Pig' 'Rat' ;
 END;
diff -r ff2724696a7d -r 8c26d4d128b3 test-data/sm19-in1.nhx
--- a/test-data/sm19-in1.nhx	Tue Oct 07 20:39:19 2025 +0000
+++ b/test-data/sm19-in1.nhx	Tue Feb 10 12:05:38 2026 +0000
@@ -1,152 +1,1 @@
-#NEXUS
-begin taxa;
-	dimensions ntax=50;
-	taxlabels
-	C019-B2_10_1[&!color=#ff0000]
-	C019-B2_13_1[&!color=#ff0000]
-	C019-B2_16_1[&!color=#ff0000]
-	C019-B2_17_3[&!color=#ff0000]
-	C019-B2_18_1[&!color=#ff0000]
-	C019-B2_1_2[&!color=#ff0000]
-	C019-B2_24_1[&!color=#ff0000]
-	C019-B2_28_1[&!color=#ff0000]
-	C019-B2_29_1[&!color=#ff0000]
-	C019-B2_31_1[&!color=#ff0000]
-	C019-B2_32_1[&!color=#ff0000]
-	C019-B2_34_1[&!color=#ff0000]
-	C019-B2_35_1[&!color=#ff0000]
-	C019-B2_42_2[&!color=#ff0000]
-	C019-B2_43_2[&!color=#ff0000]
-	C019-B2_45_1[&!color=#ff0000]
-	C019-B2_46_2[&!color=#ff0000]
-	C019-B2_47_3[&!color=#ff0000]
-	C019-B2_4_1[&!color=#ff0000]
-	C019-B2_52_1[&!color=#ff0000]
-	C019-B2_53_1[&!color=#ff0000]
-	C019-B2_54_1[&!color=#ff0000]
-	C019-B2_5_1[&!color=#ff0000]
-	C019-B2_6_3[&!color=#ff0000]
-	C019-B2_9_1[&!color=#ff0000]
-	C019-S2_10_1[&!color=#0000ff]
-	C019-S2_11_1[&!color=#0000ff]
-	C019-S2_12_2[&!color=#0000ff]
-	C019-S2_13_1[&!color=#0000ff]
-	C019-S2_14_1[&!color=#0000ff]
-	C019-S2_15_4[&!color=#0000ff]
-	C019-S2_16_1[&!color=#0000ff]
-	C019-S2_17_1[&!color=#0000ff]
-	C019-S2_18_2[&!color=#0000ff]
-	C019-S2_19_1[&!color=#0000ff]
-	C019-S2_1_1[&!color=#0000ff]
-	C019-S2_20_2[&!color=#0000ff]
-	C019-S2_21_1[&!color=#0000ff]
-	C019-S2_22_1[&!color=#0000ff]
-	C019-S2_23_2[&!color=#0000ff]
-	C019-S2_24_1[&!color=#0000ff]
-	C019-S2_25_2[&!color=#0000ff]
-	C019-S2_2_1[&!color=#0000ff]
-	C019-S2_3_1[&!color=#0000ff]
-	C019-S2_4_1[&!color=#0000ff]
-	C019-S2_5_1[&!color=#0000ff]
-	C019-S2_6_1[&!color=#0000ff]
-	C019-S2_7_1[&!color=#0000ff]
-	C019-S2_8_1[&!color=#0000ff]
-	C019-S2_9_1[&!color=#0000ff]
-;
-end;
-
-begin trees;
-	tree tree_1 = [&R] ((((((C019-B2_35_1:0.005858,C019-B2_52_1:0.001773):9.4E-4,((((((C019-B2_28_1:0.002896,C019-B2_29_1:9.09E-4):0.004372,C019-B2_31_1:0.003387):0.001252,C019-S2_9_1:0.001965):4.28E-4,C019-B2_34_1:0.003365):0.00173,C019-S2_2_1:0.011763):5.94E-4,((((C019-B2_4_1:0.002924,C019-B2_6_3:8.81E-4):0.001821,C019-B2_5_1:0.001994):0.006052,C019-S2_1_1:0.011533):0.002707,((C019-S2_4_1:0.006447,C019-S2_6_1:0.00696):0.001115,C019-S2_7_1:0.004624):0.003256):0.001452):0.002006):3.96E-4,((C019-S2_10_1:0.005429,C019-S2_12_2:3.52E-4):9.31E-4,C019-B2_42_2:9.87E-4):6.51E-4):5.28E-4,(C019-B2_53_1:0.002654,C019-B2_54_1:0.001151):0.002202):3.98E-4,((((((C019-B2_9_1:0.003599,C019-B2_10_1:0.002149):0.003701,C019-B2_1_2:0.011845):0.001658,C019-S2_3_1:0.009874):1.58E-4,C019-S2_5_1:0.009998):2.67E-4,(((C019-B2_17_3:0.0,C019-S2_22_1:0.0):6.76E-4,C019-B2_16_1:0.003129):2.62E-4,(((((C019-B2_18_1:0.0,C019-S2_25_2:0.0):3.0E-5,C019-S2_24_1:-3.0E-5):7.69E-4,C019-S2_23_2:0.003047):4.93E-4,(((((C019-B2_24_1:0.004304,C019-S2_19_1:-0.002103):0.00459,C019-S2_17_1:0.00129):0.002822,C019-S2_18_2:0.004477):8.52E-4,C019-S2_21_1:0.001446):8.3E-4,C019-S2_20_2:0.003028):0.002252):0.001275,C019-B2_13_1:0.006181):9.2E-4):0.003349):0.001411,C019-S2_13_1:-4.68E-4):0.001963):3.46E-4,(((C019-B2_45_1:8.37E-4,C019-S2_8_1:0.006794):0.001393,C019-S2_14_1:5.17E-4):3.77E-4,(((C019-B2_32_1:0.005635,C019-B2_43_2:0.001995):9.13E-4,C019-S2_11_1:0.002993):5.52E-4,(((C019-B2_46_2:0.0,C019-S2_15_4:0.0):0.001576,C019-S2_16_1:0.002229):0.001073,C019-B2_47_3:8.77E-4):8.62E-4):7.32E-4):3.46E-4);
-end;
-
-begin figtree;
-	set appearance.backgroundColorAttribute="Default";
-	set appearance.backgroundColour=#ffffff;
-	set appearance.branchColorAttribute="User selection";
-	set appearance.branchColorGradient=false;
-	set appearance.branchLineWidth=1.0;
-	set appearance.branchMinLineWidth=0.0;
-	set appearance.branchWidthAttribute="Fixed";
-	set appearance.foregroundColour=#000000;
-	set appearance.hilightingGradient=false;
-	set appearance.selectionColour=#2d3680;
-	set branchLabels.colorAttribute="User selection";
-	set branchLabels.displayAttribute="Branch times";
-	set branchLabels.fontName="sansserif";
-	set branchLabels.fontSize=8;
-	set branchLabels.fontStyle=0;
-	set branchLabels.isShown=false;
-	set branchLabels.significantDigits=4;
-	set layout.expansion=0;
-	set layout.layoutType="RECTILINEAR";
-	set layout.zoom=0;
-	set legend.attribute=null;
-	set legend.fontSize=10.0;
-	set legend.isShown=false;
-	set legend.significantDigits=4;
-	set nodeBars.barWidth=4.0;
-	set nodeBars.displayAttribute=null;
-	set nodeBars.isShown=false;
-	set nodeLabels.colorAttribute="User selection";
-	set nodeLabels.displayAttribute="Node ages";
-	set nodeLabels.fontName="sansserif";
-	set nodeLabels.fontSize=8;
-	set nodeLabels.fontStyle=0;
-	set nodeLabels.isShown=false;
-	set nodeLabels.significantDigits=4;
-	set nodeShapeExternal.colourAttribute="User selection";
-	set nodeShapeExternal.isShown=false;
-	set nodeShapeExternal.minSize=10.0;
-	set nodeShapeExternal.scaleType=Width;
-	set nodeShapeExternal.shapeType=Circle;
-	set nodeShapeExternal.size=4.0;
-	set nodeShapeExternal.sizeAttribute="Fixed";
-	set nodeShapeInternal.colourAttribute="User selection";
-	set nodeShapeInternal.isShown=false;
-	set nodeShapeInternal.minSize=10.0;
-	set nodeShapeInternal.scaleType=Width;
-	set nodeShapeInternal.shapeType=Circle;
-	set nodeShapeInternal.size=4.0;
-	set nodeShapeInternal.sizeAttribute="Fixed";
-	set polarLayout.alignTipLabels=false;
-	set polarLayout.angularRange=0;
-	set polarLayout.rootAngle=0;
-	set polarLayout.rootLength=100;
-	set polarLayout.showRoot=true;
-	set radialLayout.spread=0.0;
-	set rectilinearLayout.alignTipLabels=false;
-	set rectilinearLayout.curvature=0;
-	set rectilinearLayout.rootLength=100;
-	set scale.offsetAge=0.0;
-	set scale.rootAge=1.0;
-	set scale.scaleFactor=1.0;
-	set scale.scaleRoot=false;
-	set scaleAxis.automaticScale=true;
-	set scaleAxis.fontSize=8.0;
-	set scaleAxis.isShown=false;
-	set scaleAxis.lineWidth=1.0;
-	set scaleAxis.majorTicks=1.0;
-	set scaleAxis.minorTicks=0.5;
-	set scaleAxis.origin=0.0;
-	set scaleAxis.reverseAxis=false;
-	set scaleAxis.showGrid=true;
-	set scaleBar.automaticScale=true;
-	set scaleBar.fontSize=10.0;
-	set scaleBar.isShown=true;
-	set scaleBar.lineWidth=1.0;
-	set scaleBar.scaleRange=0.0;
-	set tipLabels.colorAttribute="User selection";
-	set tipLabels.displayAttribute="Names";
-	set tipLabels.fontName="sansserif";
-	set tipLabels.fontSize=8;
-	set tipLabels.fontStyle=0;
-	set tipLabels.isShown=true;
-	set tipLabels.significantDigits=4;
-	set trees.order=false;
-	set trees.orderType="increasing";
-	set trees.rooting=false;
-	set trees.rootingType="User Selection";
-	set trees.transform=false;
-	set trees.transformType="cladogram";
-end;
-
+((((((C019-B2_35_1:0.005858,C019-B2_52_1:0.001773):0.00094,((((((C019-B2_28_1:0.002896,C019-B2_29_1:0.000909):0.004372,C019-B2_31_1:0.003387):0.001252,C019-S2_9_1:0.001965):0.000428,C019-B2_34_1:0.003365):0.00173,C019-S2_2_1:0.011763):0.000594,((((C019-B2_4_1:0.002924,C019-B2_6_3:0.000881):0.001821,C019-B2_5_1:0.001994):0.006052,C019-S2_1_1:0.011533):0.002707,((C019-S2_4_1:0.006447,C019-S2_6_1:0.00696):0.001115,C019-S2_7_1:0.004624):0.003256):0.001452):0.002006):0.000396,((C019-S2_10_1:0.005429,C019-S2_12_2:0.000352):0.000931,C019-B2_42_2:0.000987):0.000651):0.000528,(C019-B2_53_1:0.002654,C019-B2_54_1:0.001151):0.002202):0.000398,((((((C019-B2_9_1:0.003599,C019-B2_10_1:0.002149):0.003701,C019-B2_1_2:0.011845):0.001658,C019-S2_3_1:0.009874):0.000158,C019-S2_5_1:0.009998):0.000267,(((C019-B2_17_3:0.0,C019-S2_22_1:0.0):0.000676,C019-B2_16_1:0.003129):0.000262,(((((C019-B2_18_1:0.0,C019-S2_25_2:0.0):0.00003,C019-S2_24_1:-0.00003):0.000769,C019-S2_23_2:0.003047):0.000493,(((((C019-B2_24_1:0.004304,C019-S2_19_1:-0.002103):0.00459,C019-S2_17_1:0.00129):0.002822,C019-S2_18_2:0.004477):0.000852,C019-S2_21_1:0.001446):0.00083,C019-S2_20_2:0.003028):0.002252):0.001275,C019-B2_13_1:0.006181):0.00092):0.003349):0.001411,C019-S2_13_1:-0.000468):0.001963):0.000346,(((C019-B2_45_1:0.000837,C019-S2_8_1:0.006794):0.001393,C019-S2_14_1:0.000517):0.000377,(((C019-B2_32_1:0.005635,C019-B2_43_2:0.001995):0.000913,C019-S2_11_1:0.002993):0.000552,(((C019-B2_46_2:0.0,C019-S2_15_4:0.0):0.001576,C019-S2_16_1:0.002229):0.001073,C019-B2_47_3:0.000877):0.000862):0.000732):0.000346)
diff -r ff2724696a7d -r 8c26d4d128b3 test-data/sm19-in2.nhx
--- a/test-data/sm19-in2.nhx	Tue Oct 07 20:39:19 2025 +0000
+++ b/test-data/sm19-in2.nhx	Tue Feb 10 12:05:38 2026 +0000
@@ -1,166 +1,1 @@
-#NEXUS
-begin taxa;
-	dimensions ntax=64;
-	taxlabels
-	C019-B3_103_1[&!color=#ff0000]
-	C019-B3_10_1[&!color=#ff0000]
-	C019-B3_121_1[&!color=#ff0000]
-	C019-B3_122_4[&!color=#ff0000]
-	C019-B3_125_1[&!color=#ff0000]
-	C019-B3_132_1[&!color=#ff0000]
-	C019-B3_140_2[&!color=#ff0000]
-	C019-B3_144_1[&!color=#ff0000]
-	C019-B3_147_1[&!color=#ff0000]
-	C019-B3_154_1[&!color=#ff0000]
-	C019-B3_162_1[&!color=#ff0000]
-	C019-B3_164_1[&!color=#ff0000]
-	C019-B3_173_1[&!color=#ff0000]
-	C019-B3_179_1[&!color=#ff0000]
-	C019-B3_180_1[&!color=#ff0000]
-	C019-B3_18_1[&!color=#ff0000]
-	C019-B3_1_1[&!color=#ff0000]
-	C019-B3_201_1[&!color=#ff0000]
-	C019-B3_211_4[&!color=#ff0000]
-	C019-B3_26_6[&!color=#ff0000]
-	C019-B3_27_1[&!color=#ff0000]
-	C019-B3_32_1[&!color=#ff0000]
-	C019-B3_37_1[&!color=#ff0000]
-	C019-B3_3_2[&!color=#ff0000]
-	C019-B3_57_1[&!color=#ff0000]
-	C019-B3_59_1[&!color=#ff0000]
-	C019-B3_61_3[&!color=#ff0000]
-	C019-B3_63_1[&!color=#ff0000]
-	C019-B3_84_1[&!color=#ff0000]
-	C019-B3_87_1[&!color=#ff0000]
-	C019-B3_94_1[&!color=#ff0000]
-	C019-B3_98_1[&!color=#ff0000]
-	C019-S3_10_3[&!color=#0000ff]
-	C019-S3_11_1[&!color=#0000ff]
-	C019-S3_12_1[&!color=#0000ff]
-	C019-S3_13_1[&!color=#0000ff]
-	C019-S3_14_1[&!color=#0000ff]
-	C019-S3_15_1[&!color=#0000ff]
-	C019-S3_16_1[&!color=#0000ff]
-	C019-S3_17_1[&!color=#0000ff]
-	C019-S3_18_1[&!color=#0000ff]
-	C019-S3_19_2[&!color=#0000ff]
-	C019-S3_1_3[&!color=#0000ff]
-	C019-S3_20_1[&!color=#0000ff]
-	C019-S3_21_1[&!color=#0000ff]
-	C019-S3_22_2[&!color=#0000ff]
-	C019-S3_23_6[&!color=#0000ff]
-	C019-S3_24_1[&!color=#0000ff]
-	C019-S3_25_1[&!color=#0000ff]
-	C019-S3_26_1[&!color=#0000ff]
-	C019-S3_27_1[&!color=#0000ff]
-	C019-S3_28_1[&!color=#0000ff]
-	C019-S3_29_1[&!color=#0000ff]
-	C019-S3_2_1[&!color=#0000ff]
-	C019-S3_30_5[&!color=#0000ff]
-	C019-S3_31_1[&!color=#0000ff]
-	C019-S3_32_1[&!color=#0000ff]
-	C019-S3_3_1[&!color=#0000ff]
-	C019-S3_4_1[&!color=#0000ff]
-	C019-S3_5_1[&!color=#0000ff]
-	C019-S3_6_1[&!color=#0000ff]
-	C019-S3_7_44[&!color=#0000ff]
-	C019-S3_8_1[&!color=#0000ff]
-	C019-S3_9_1[&!color=#0000ff]
-;
-end;
-
-begin trees;
-	tree tree_1 = [&R] (((((((C019-S3_30_5:0.001628,C019-S3_29_1:0.006003):0.00113,(C019-B3_173_1:0.001171,C019-S3_28_1:0.002634):0.001744):8.3E-4,C019-B3_132_1:0.014016):5.86E-4,((C019-S3_25_1:0.002323,C019-S3_26_1:0.001482):9.35E-4,C019-B3_144_1:0.004793):0.001476):5.2E-4,((C019-B3_140_2:0.005006,C019-B3_211_4:7.09E-4):0.005792,C019-S3_24_1:0.003793):6.51E-4):3.29E-4,((((((C019-B3_180_1:0.007012,C019-S3_12_1:0.002539):0.001059,C019-B3_164_1:0.004685):0.001059,C019-B3_201_1:0.002755):4.7E-4,C019-S3_27_1:0.004308):5.29E-4,(C019-B3_179_1:0.00111,C019-B3_162_1:0.006521):0.001397):4.5E-4,(((C019-B3_98_1:0.00603,C019-B3_84_1:0.011255):0.001462,C019-B3_3_2:0.01022):0.004778,(((((C019-B3_122_4:-1.5E-5,C019-B3_121_1:0.003821):1.07E-4,(((C019-S3_6_1:3.19E-4,C019-S3_5_1:0.003493):2.06E-4,C019-S3_4_1:0.003609):1.56E-4,C019-S3_7_44:-1.63E-4):0.001868):8.3E-5,C019-S3_2_1:0.003743):9.49E-4,C019-S3_3_1:9.47E-4):1.32E-4,((((((C019-B3_87_1:0.004026,C019-B3_94_1:0.003649):0.001868,C019-S3_9_1:0.001947):5.6E-5,C019-S3_8_1:0.001847):0.002662,C019-S3_10_3:0.003074):0.001087,C019-B3_103_1:0.002733):2.29E-4,(C019-S3_1_3:0.003978,C019-B3_125_1:0.003697):9.13E-4):4.97E-4):0.006645):7.82E-4):8.25E-4):5.47E-4,((((C019-S3_22_2:9.84E-4,C019-S3_23_6:0.005041):0.001644,(((((((((C019-B3_32_1:0.001955,C019-S3_15_1:-5.5E-5):9.11E-4,C019-B3_37_1:9.97E-4):0.001209,C019-B3_57_1:0.002666):0.001047,C019-B3_59_1:0.001825):0.001321,(C019-B3_26_6:-2.4E-5,C019-B3_27_1:2.4E-5):0.006853):0.001793,C019-B3_10_1:0.009272):0.001166,((C019-S3_19_2:7.58E-4,C019-S3_17_1:0.003048):0.001952,C019-S3_11_1:0.007625):0.001734):0.001109,C019-B3_147_1:0.00437):0.001515,(((C019-S3_32_1:0.009024,C019-S3_31_1:0.002453):0.007605,C019-B3_1_1:0.014729):0.003341,(C019-S3_14_1:0.002908,C019-S3_13_1:0.004722):0.006888):0.001642):0.00149):2.85E-4,(((C019-S3_20_1:4.17E-4,C019-S3_21_1:0.001505):0.001098,C019-S3_16_1:0.00369):0.00156,((C019-B3_61_3:7.33E-4,C019-B3_63_1:0.006898):0.003303,C019-B3_18_1:0.0063):0.00288):7.85E-4):1.97E-4,(C019-S3_18_1:3.32E-4,C019-B3_154_1:0.00368):0.001664):5.47E-4);
-end;
-
-begin figtree;
-	set appearance.backgroundColorAttribute="Default";
-	set appearance.backgroundColour=#ffffff;
-	set appearance.branchColorAttribute="User selection";
-	set appearance.branchColorGradient=false;
-	set appearance.branchLineWidth=1.0;
-	set appearance.branchMinLineWidth=0.0;
-	set appearance.branchWidthAttribute="Fixed";
-	set appearance.foregroundColour=#000000;
-	set appearance.hilightingGradient=false;
-	set appearance.selectionColour=#2d3680;
-	set branchLabels.colorAttribute="User selection";
-	set branchLabels.displayAttribute="Branch times";
-	set branchLabels.fontName="sansserif";
-	set branchLabels.fontSize=8;
-	set branchLabels.fontStyle=0;
-	set branchLabels.isShown=false;
-	set branchLabels.significantDigits=4;
-	set layout.expansion=0;
-	set layout.layoutType="RECTILINEAR";
-	set layout.zoom=0;
-	set legend.attribute=null;
-	set legend.fontSize=10.0;
-	set legend.isShown=false;
-	set legend.significantDigits=4;
-	set nodeBars.barWidth=4.0;
-	set nodeBars.displayAttribute=null;
-	set nodeBars.isShown=false;
-	set nodeLabels.colorAttribute="User selection";
-	set nodeLabels.displayAttribute="Node ages";
-	set nodeLabels.fontName="sansserif";
-	set nodeLabels.fontSize=8;
-	set nodeLabels.fontStyle=0;
-	set nodeLabels.isShown=false;
-	set nodeLabels.significantDigits=4;
-	set nodeShapeExternal.colourAttribute="User selection";
-	set nodeShapeExternal.isShown=false;
-	set nodeShapeExternal.minSize=10.0;
-	set nodeShapeExternal.scaleType=Width;
-	set nodeShapeExternal.shapeType=Circle;
-	set nodeShapeExternal.size=4.0;
-	set nodeShapeExternal.sizeAttribute="Fixed";
-	set nodeShapeInternal.colourAttribute="User selection";
-	set nodeShapeInternal.isShown=false;
-	set nodeShapeInternal.minSize=10.0;
-	set nodeShapeInternal.scaleType=Width;
-	set nodeShapeInternal.shapeType=Circle;
-	set nodeShapeInternal.size=4.0;
-	set nodeShapeInternal.sizeAttribute="Fixed";
-	set polarLayout.alignTipLabels=false;
-	set polarLayout.angularRange=0;
-	set polarLayout.rootAngle=0;
-	set polarLayout.rootLength=100;
-	set polarLayout.showRoot=true;
-	set radialLayout.spread=0.0;
-	set rectilinearLayout.alignTipLabels=false;
-	set rectilinearLayout.curvature=0;
-	set rectilinearLayout.rootLength=100;
-	set scale.offsetAge=0.0;
-	set scale.rootAge=1.0;
-	set scale.scaleFactor=1.0;
-	set scale.scaleRoot=false;
-	set scaleAxis.automaticScale=true;
-	set scaleAxis.fontSize=8.0;
-	set scaleAxis.isShown=false;
-	set scaleAxis.lineWidth=1.0;
-	set scaleAxis.majorTicks=1.0;
-	set scaleAxis.minorTicks=0.5;
-	set scaleAxis.origin=0.0;
-	set scaleAxis.reverseAxis=false;
-	set scaleAxis.showGrid=true;
-	set scaleBar.automaticScale=true;
-	set scaleBar.fontSize=10.0;
-	set scaleBar.isShown=true;
-	set scaleBar.lineWidth=1.0;
-	set scaleBar.scaleRange=0.0;
-	set tipLabels.colorAttribute="User selection";
-	set tipLabels.displayAttribute="Names";
-	set tipLabels.fontName="sansserif";
-	set tipLabels.fontSize=8;
-	set tipLabels.fontStyle=0;
-	set tipLabels.isShown=true;
-	set tipLabels.significantDigits=4;
-	set trees.order=false;
-	set trees.orderType="increasing";
-	set trees.rooting=false;
-	set trees.rootingType="User Selection";
-	set trees.transform=false;
-	set trees.transformType="cladogram";
-end;
-
+(((((((C019-S3_30_5:0.001628,C019-S3_29_1:0.006003):0.00113,(C019-B3_173_1:0.001171,C019-S3_28_1:0.002634):0.001744):8.3E-4,C019-B3_132_1:0.014016):5.86E-4,((C019-S3_25_1:0.002323,C019-S3_26_1:0.001482):9.35E-4,C019-B3_144_1:0.004793):0.001476):5.2E-4,((C019-B3_140_2:0.005006,C019-B3_211_4:7.09E-4):0.005792,C019-S3_24_1:0.003793):6.51E-4):3.29E-4,((((((C019-B3_180_1:0.007012,C019-S3_12_1:0.002539):0.001059,C019-B3_164_1:0.004685):0.001059,C019-B3_201_1:0.002755):4.7E-4,C019-S3_27_1:0.004308):5.29E-4,(C019-B3_179_1:0.00111,C019-B3_162_1:0.006521):0.001397):4.5E-4,(((C019-B3_98_1:0.00603,C019-B3_84_1:0.011255):0.001462,C019-B3_3_2:0.01022):0.004778,(((((C019-B3_122_4:-1.5E-5,C019-B3_121_1:0.003821):1.07E-4,(((C019-S3_6_1:3.19E-4,C019-S3_5_1:0.003493):2.06E-4,C019-S3_4_1:0.003609):1.56E-4,C019-S3_7_44:-1.63E-4):0.001868):8.3E-5,C019-S3_2_1:0.003743):9.49E-4,C019-S3_3_1:9.47E-4):1.32E-4,((((((C019-B3_87_1:0.004026,C019-B3_94_1:0.003649):0.001868,C019-S3_9_1:0.001947):5.6E-5,C019-S3_8_1:0.001847):0.002662,C019-S3_10_3:0.003074):0.001087,C019-B3_103_1:0.002733):2.29E-4,(C019-S3_1_3:0.003978,C019-B3_125_1:0.003697):9.13E-4):4.97E-4):0.006645):7.82E-4):8.25E-4):5.47E-4,((((C019-S3_22_2:9.84E-4,C019-S3_23_6:0.005041):0.001644,(((((((((C019-B3_32_1:0.001955,C019-S3_15_1:-5.5E-5):9.11E-4,C019-B3_37_1:9.97E-4):0.001209,C019-B3_57_1:0.002666):0.001047,C019-B3_59_1:0.001825):0.001321,(C019-B3_26_6:-2.4E-5,C019-B3_27_1:2.4E-5):0.006853):0.001793,C019-B3_10_1:0.009272):0.001166,((C019-S3_19_2:7.58E-4,C019-S3_17_1:0.003048):0.001952,C019-S3_11_1:0.007625):0.001734):0.001109,C019-B3_147_1:0.00437):0.001515,(((C019-S3_32_1:0.009024,C019-S3_31_1:0.002453):0.007605,C019-B3_1_1:0.014729):0.003341,(C019-S3_14_1:0.002908,C019-S3_13_1:0.004722):0.006888):0.001642):0.00149):2.85E-4,(((C019-S3_20_1:4.17E-4,C019-S3_21_1:0.001505):0.001098,C019-S3_16_1:0.00369):0.00156,((C019-B3_61_3:7.33E-4,C019-B3_63_1:0.006898):0.003303,C019-B3_18_1:0.0063):0.00288):7.85E-4):1.97E-4,(C019-S3_18_1:3.32E-4,C019-B3_154_1:0.00368):0.001664):5.47E-4)