Mercurial > repos > iuc > hyphy_annotate

diff test-data/sm19-in2.nhx @ 0:df56795c3d89 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author iuc
date Tue, 20 Apr 2021 10:29:30 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sm19-in2.nhx	Tue Apr 20 10:29:30 2021 +0000
@@ -0,0 +1,166 @@
+#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;
+