Mercurial > repos > iuc > hyphy_bgm

comparison test-data/sm19-in2.nhx @ 0:bf97cacc1a55 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author iuc
date Wed, 21 Aug 2019 12:23:09 -0400
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comparison
equal deleted inserted replaced
-1:000000000000 0:bf97cacc1a55
1 #NEXUS
2 begin taxa;
3 dimensions ntax=64;
4 taxlabels
5 C019-B3_103_1[&!color=#ff0000]
6 C019-B3_10_1[&!color=#ff0000]
7 C019-B3_121_1[&!color=#ff0000]
8 C019-B3_122_4[&!color=#ff0000]
9 C019-B3_125_1[&!color=#ff0000]
10 C019-B3_132_1[&!color=#ff0000]
11 C019-B3_140_2[&!color=#ff0000]
12 C019-B3_144_1[&!color=#ff0000]
13 C019-B3_147_1[&!color=#ff0000]
14 C019-B3_154_1[&!color=#ff0000]
15 C019-B3_162_1[&!color=#ff0000]
16 C019-B3_164_1[&!color=#ff0000]
17 C019-B3_173_1[&!color=#ff0000]
18 C019-B3_179_1[&!color=#ff0000]
19 C019-B3_180_1[&!color=#ff0000]
20 C019-B3_18_1[&!color=#ff0000]
21 C019-B3_1_1[&!color=#ff0000]
22 C019-B3_201_1[&!color=#ff0000]
23 C019-B3_211_4[&!color=#ff0000]
24 C019-B3_26_6[&!color=#ff0000]
25 C019-B3_27_1[&!color=#ff0000]
26 C019-B3_32_1[&!color=#ff0000]
27 C019-B3_37_1[&!color=#ff0000]
28 C019-B3_3_2[&!color=#ff0000]
29 C019-B3_57_1[&!color=#ff0000]
30 C019-B3_59_1[&!color=#ff0000]
31 C019-B3_61_3[&!color=#ff0000]
32 C019-B3_63_1[&!color=#ff0000]
33 C019-B3_84_1[&!color=#ff0000]
34 C019-B3_87_1[&!color=#ff0000]
35 C019-B3_94_1[&!color=#ff0000]
36 C019-B3_98_1[&!color=#ff0000]
37 C019-S3_10_3[&!color=#0000ff]
38 C019-S3_11_1[&!color=#0000ff]
39 C019-S3_12_1[&!color=#0000ff]
40 C019-S3_13_1[&!color=#0000ff]
41 C019-S3_14_1[&!color=#0000ff]
42 C019-S3_15_1[&!color=#0000ff]
43 C019-S3_16_1[&!color=#0000ff]
44 C019-S3_17_1[&!color=#0000ff]
45 C019-S3_18_1[&!color=#0000ff]
46 C019-S3_19_2[&!color=#0000ff]
47 C019-S3_1_3[&!color=#0000ff]
48 C019-S3_20_1[&!color=#0000ff]
49 C019-S3_21_1[&!color=#0000ff]
50 C019-S3_22_2[&!color=#0000ff]
51 C019-S3_23_6[&!color=#0000ff]
52 C019-S3_24_1[&!color=#0000ff]
53 C019-S3_25_1[&!color=#0000ff]
54 C019-S3_26_1[&!color=#0000ff]
55 C019-S3_27_1[&!color=#0000ff]
56 C019-S3_28_1[&!color=#0000ff]
57 C019-S3_29_1[&!color=#0000ff]
58 C019-S3_2_1[&!color=#0000ff]
59 C019-S3_30_5[&!color=#0000ff]
60 C019-S3_31_1[&!color=#0000ff]
61 C019-S3_32_1[&!color=#0000ff]
62 C019-S3_3_1[&!color=#0000ff]
63 C019-S3_4_1[&!color=#0000ff]
64 C019-S3_5_1[&!color=#0000ff]
65 C019-S3_6_1[&!color=#0000ff]
66 C019-S3_7_44[&!color=#0000ff]
67 C019-S3_8_1[&!color=#0000ff]
68 C019-S3_9_1[&!color=#0000ff]
69 ;
70 end;
71
72 begin trees;
73 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);
74 end;
75
76 begin figtree;
77 set appearance.backgroundColorAttribute="Default";
78 set appearance.backgroundColour=#ffffff;
79 set appearance.branchColorAttribute="User selection";
80 set appearance.branchColorGradient=false;
81 set appearance.branchLineWidth=1.0;
82 set appearance.branchMinLineWidth=0.0;
83 set appearance.branchWidthAttribute="Fixed";
84 set appearance.foregroundColour=#000000;
85 set appearance.hilightingGradient=false;
86 set appearance.selectionColour=#2d3680;
87 set branchLabels.colorAttribute="User selection";
88 set branchLabels.displayAttribute="Branch times";
89 set branchLabels.fontName="sansserif";
90 set branchLabels.fontSize=8;
91 set branchLabels.fontStyle=0;
92 set branchLabels.isShown=false;
93 set branchLabels.significantDigits=4;
94 set layout.expansion=0;
95 set layout.layoutType="RECTILINEAR";
96 set layout.zoom=0;
97 set legend.attribute=null;
98 set legend.fontSize=10.0;
99 set legend.isShown=false;
100 set legend.significantDigits=4;
101 set nodeBars.barWidth=4.0;
102 set nodeBars.displayAttribute=null;
103 set nodeBars.isShown=false;
104 set nodeLabels.colorAttribute="User selection";
105 set nodeLabels.displayAttribute="Node ages";
106 set nodeLabels.fontName="sansserif";
107 set nodeLabels.fontSize=8;
108 set nodeLabels.fontStyle=0;
109 set nodeLabels.isShown=false;
110 set nodeLabels.significantDigits=4;
111 set nodeShapeExternal.colourAttribute="User selection";
112 set nodeShapeExternal.isShown=false;
113 set nodeShapeExternal.minSize=10.0;
114 set nodeShapeExternal.scaleType=Width;
115 set nodeShapeExternal.shapeType=Circle;
116 set nodeShapeExternal.size=4.0;
117 set nodeShapeExternal.sizeAttribute="Fixed";
118 set nodeShapeInternal.colourAttribute="User selection";
119 set nodeShapeInternal.isShown=false;
120 set nodeShapeInternal.minSize=10.0;
121 set nodeShapeInternal.scaleType=Width;
122 set nodeShapeInternal.shapeType=Circle;
123 set nodeShapeInternal.size=4.0;
124 set nodeShapeInternal.sizeAttribute="Fixed";
125 set polarLayout.alignTipLabels=false;
126 set polarLayout.angularRange=0;
127 set polarLayout.rootAngle=0;
128 set polarLayout.rootLength=100;
129 set polarLayout.showRoot=true;
130 set radialLayout.spread=0.0;
131 set rectilinearLayout.alignTipLabels=false;
132 set rectilinearLayout.curvature=0;
133 set rectilinearLayout.rootLength=100;
134 set scale.offsetAge=0.0;
135 set scale.rootAge=1.0;
136 set scale.scaleFactor=1.0;
137 set scale.scaleRoot=false;
138 set scaleAxis.automaticScale=true;
139 set scaleAxis.fontSize=8.0;
140 set scaleAxis.isShown=false;
141 set scaleAxis.lineWidth=1.0;
142 set scaleAxis.majorTicks=1.0;
143 set scaleAxis.minorTicks=0.5;
144 set scaleAxis.origin=0.0;
145 set scaleAxis.reverseAxis=false;
146 set scaleAxis.showGrid=true;
147 set scaleBar.automaticScale=true;
148 set scaleBar.fontSize=10.0;
149 set scaleBar.isShown=true;
150 set scaleBar.lineWidth=1.0;
151 set scaleBar.scaleRange=0.0;
152 set tipLabels.colorAttribute="User selection";
153 set tipLabels.displayAttribute="Names";
154 set tipLabels.fontName="sansserif";
155 set tipLabels.fontSize=8;
156 set tipLabels.fontStyle=0;
157 set tipLabels.isShown=true;
158 set tipLabels.significantDigits=4;
159 set trees.order=false;
160 set trees.orderType="increasing";
161 set trees.rooting=false;
162 set trees.rootingType="User Selection";
163 set trees.transform=false;
164 set trees.transformType="cladogram";
165 end;
166