Mercurial > repos > iuc > hyphy_busted
changeset 36:17eabaa1198c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy commit db3cc714a88f1c34dfa888b749a30b17bc898ee9
| author | iuc |
|---|---|
| date | Tue, 10 Feb 2026 12:05:59 +0000 |
| parents | 3169a46cd44c |
| children | |
| files | hyphy_busted.xml macros.xml test-data/absrel-in1.fa test-data/annotate-out1-full.nhx test-data/cln-stop-codons.fa test-data/relax-in2.nex test-data/sm19-in1.nhx test-data/sm19-in2.nhx |
| diffstat | 8 files changed, 17 insertions(+), 327 deletions(-) [+] |
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--- a/hyphy_busted.xml Tue Oct 07 20:39:51 2025 +0000 +++ b/hyphy_busted.xml Tue Feb 10 12:05:59 2026 +0000 @@ -245,7 +245,7 @@ MSS Methodology --------------- -BUSTED can also incorporate models of selection on synonymous substitutions (MSS models). This is a new comparative framework for estimating selection on synonymous substitutions. These models account for selection by partitioning synonymous substitutions into multiple classes and estimating relative substitution rates for each, while also considering confounders like mutation bias. This framework allows for the study of selection on synonymous substitutions in diverse taxa without prior assumptions about the driving forces. For more information, please see the source publication: http://pubmed.ncbi.nlm.nih.gov/40129111/ +BUSTED can also incorporate models of selection on synonymous substitutions (MSS models). This is a new comparative framework for estimating selection on synonymous substitutions. These models account for selection by partitioning synonymous substitutions into multiple classes and estimating relative substitution rates for each, while also considering confounders like mutation bias. This framework allows for the study of selection on synonymous substitutions in diverse taxa without prior assumptions about the driving forces. For more information, please see the source publication: https://doi.org/10.1093/molbev/msaf068 Input -----
--- a/macros.xml Tue Oct 07 20:39:51 2025 +0000 +++ b/macros.xml Tue Feb 10 12:05:59 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>
--- a/test-data/absrel-in1.fa Tue Oct 07 20:39:51 2025 +0000 +++ b/test-data/absrel-in1.fa Tue Feb 10 12:05:59 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
--- a/test-data/annotate-out1-full.nhx Tue Oct 07 20:39:51 2025 +0000 +++ b/test-data/annotate-out1-full.nhx Tue Feb 10 12:05:59 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cln-stop-codons.fa Tue Feb 10 12:05:59 2026 +0000 @@ -0,0 +1,6 @@ +>GoodSeq +ATGGCGACC +>StopSeq +ATGTAGGCG +>GoodSeqDup +ATGGCGACC \ No newline at end of file
--- a/test-data/relax-in2.nex Tue Oct 07 20:39:51 2025 +0000 +++ b/test-data/relax-in2.nex Tue Feb 10 12:05:59 2026 +0000 @@ -6,7 +6,7 @@ ] BEGIN TAXA; - DIMENSIONS NTAX = 10; + DIMENSIONS NTAX = 4; TAXLABELS 'Baboon' 'Cow' 'Pig' 'Rat' ; END;
--- a/test-data/sm19-in1.nhx Tue Oct 07 20:39:51 2025 +0000 +++ b/test-data/sm19-in1.nhx Tue Feb 10 12:05:59 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)
--- a/test-data/sm19-in2.nhx Tue Oct 07 20:39:51 2025 +0000 +++ b/test-data/sm19-in2.nhx Tue Feb 10 12:05:59 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)