hivtree: Phylogenetic Tree of 193 HIV-1 Sequences

Description Usage Format Source References Examples

Description

This data set describes an estimated clock-like phylogeny of 193 HIV-1 group M sequences sampled in the Democratic Republic of Congo.

Usage

1
2

Format

hivtree.newick is a string with the tree in Newick format. The data frame hivtree.table contains the corresponding internode distances.

Source

This is a data example from Strimmer and Pybus (2001).

References

Strimmer, K. and Pybus, O. G. (2001) Exploring the demographic history of DNA sequences using the generalized skyline plot. Molecular Biology and Evolution, 18, 2298–2305.

Examples

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# example tree in NH format (a string)
data("hivtree.newick") 
hivtree.newick

# generate file "hivtree.phy" in working directory
cat(hivtree.newick, file = "hivtree.phy", sep = "\n")
tree.hiv <- read.tree("hivtree.phy") # load tree
unlink("hivtree.phy") # delete the file "hivtree.phy"

plot(tree.hiv)

# table with list of internode distances
data("hivtree.table") 
hivtree.table


# construct coalescence intervals
ci <- coalescent.intervals(tree.hiv) # from tree
ci <- coalescent.intervals(hivtree.table$size) #from intervals
ci

Example output

[1] "(((((((((((A97DCA1EQTB52:0.077166,A97DCA1MBFE185:0.077166):0.008836,(A97DCA1MBS12:0.049821,A97DCA1MBS30:0.049821):0.036182):0.010266,A97DCA1SJDS17:0.096270):0.003116,(A97DCA1KCD9:0.083123,A97DCA1KTB185:0.083123):0.016262):0.002506,A97DCA1KFE58:0.101892):0.046439,(A97DCA1KP18:0.119083,(A97DCA1KP28:0.092297,(A97DCA1KP78:0.090247,A97DCA1MBS63:0.090247):0.002049):0.026786):0.029248):0.003031,(((A97DCA2KP82:0.050058,A97DCA2KP86:0.050058):0.067136,A97DCA2MBCD5:0.117195):0.027195,((((A97DCEQS1:0.101879,A97DCKFE326:0.101879):0.014125,A97DCMBS32:0.116003):0.019791,(A97DCEQS18:0.091575,A97DCKP72:0.091575):0.044219):0.000001,((((((A97DCEQS25:0.078087,A97DCKS34:0.078087):0.036307,A97DCKS47:0.114394):0.006016,(A97DCKMST147:0.103929,(A97DCKMST89:0.091417,A97DCKTB6:0.091417):0.012512):0.016482):0.000086,((((A97DCEQTB44:0.108703,((A97DCKDS85:0.080907,A97DCMBS26:0.080907):0.023577,A97DCKTB79:0.104485):0.004218):0.005284,(A97DCKTB118:0.090239,A97DCKTB132:0.090239):0.023749):0.000575,(A97DCKCC4:0.111547,(((A97DCKP25:0.087787,A97DCKTB7:0.087787):0.018267,A97DCMBS9:0.106055):0.001233,(A97DCKS36:0.094007,A97DCKTB37:0.094007):0.013281):0.004259):0.003015):0.004429,(((A97DCKCD6:0.082435,(A97DCMBFE149:0.069344,A97DCMBFE247:0.069344):0.013092):0.000001,((A97DCKFE198:0.065151,A97DCKP77:0.065151):0.013338,(A97DCKMST52:0.070506,A97DCKS7:0.070506):0.007982):0.003946):0.012315,A97DCKTB36:0.094750):0.024241):0.001504):0.007409,(((A97DCKP36:0.107066,A97DCKTB16:0.107066):0.009046,(A97DCMBS28:0.105021,A97DCMBTB54:0.105021):0.011089):0.011793,(((A97DCKP5:0.113319,(((A97DCMBFE155:0.079795,(A97DCMBFE244:0.057624,A97DCMBFE78:0.057624):0.022171):0.017550,A97DCMBS7:0.097346):0.000001,A97DCMBS341:0.097346):0.015975):0.000815,((A97DCKTB157:0.094386,(A97DCMBP2:0.070132,A97DCMBS4:0.070132):0.024254):0.005564,A97DCMBTB29:0.099950):0.014184):0.007922,A97DCMBDS17:0.122057):0.005848):0.000001):0.000001,((((((A97DCEQS45:0.059728,A97DCEQS49:0.059728):0.021193,A97DCKS56:0.080921):0.007725,A97DCEQTB14:0.088646):0.028870,A97DCKTB20:0.117516):0.000214,A97DCKTB44:0.117729):0.004694,((((((A97DCKCC2:0.021163,A97DCKCC3:0.021163):0.050237,A97DCKTB13:0.071400):0.033783,A97DCKMST140:0.105183):0.004152,(A97DCKMST121:0.101085,((A97DCKP43:0.069726,A97DCKP79:0.069726):0.025382,(A97DCKS55:0.094174,A97DCKTB124:0.094174):0.000933):0.005977):0.008249):0.004330,((A97DCKFE4:0.067768,A97DCKS10:0.067768):0.012439,A97DCKTB48:0.080208):0.033457):0.000001,((A97DCKFE288:0.080093,(A97DCMBFE5:0.063013,A97DCSJFE26:0.063013):0.017081):0.009386,(A97DCKMST50:0.082718,A97DCKS14:0.082718):0.006759):0.024185):0.008758):0.005482):0.007891):0.008594):0.006973):0.029972,(((U97DCKFE267:0.068246,U97DCKTB119:0.068246):0.012677,U97DCMBFE250:0.080923):0.085378,U97DCKMST91:0.166301):0.015033):0.015665,(((E97DCEQS21:0.083436,(E97DCEQS5:0.077774,E97DCKP14:0.077774):0.005662):0.007143,E97DCEQTB60:0.090579):0.044516,(U97DCKFE45:0.089540,U97DCKTB49:0.089540):0.045555):0.061904):0.000001,(((D97DCD1KCD4:0.088821,D97DCD1KMST126:0.088821):0.036417,((((((((((D97DCD1KS2:0.059334,D97DCKP54:0.059334):0.024482,D97DCKP44:0.083817):0.006959,D97DCKTB181:0.090775):0.006373,(D97DCMBS55:0.057578,D97DCMBS56:0.057578):0.039570):0.004811,(D97DCD2KTB23:0.096432,D97DCKMST66:0.096432):0.005529):0.000001,(D97DCKMST30:0.058580,D97DCKP1:0.058580):0.043380):0.002729,((D97DCKS11:0.081263,D97DCKTB27:0.081263):0.013417,(D97DCKTB4:0.094129,D97DCMBS35:0.094129):0.000553):0.010008):0.003638,(D97DCD2KS26:0.104385,D97DCKS15:0.104385):0.003943):0.010453,(D97DCKS39:0.103058,D97DCMBS342:0.103058):0.015722):0.001709,(D97DCKMST144:0.103877,D97DCKS29:0.103877):0.016613):0.004749):0.007051,D97DCKFE53:0.132289):0.064709):0.012112,((((C97DCKCD11:0.130468,((((C97DCKFE372:0.081730,C97DCMBFE92:0.081730):0.023286,((((C97DCKTB110:0.096163,(C97DCMBFE14:0.093774,(C97DCMBFE300:0.089218,(C97DCMBFE34:0.069633,C97DCMBS37:0.069633):0.019585):0.004557):0.002390):0.003304,(C97DCMBFE61:0.087463,C97DCMBTB58:0.087463):0.012005):0.002932,C97DCMBTB11:0.102399):0.002618,C97DCMBTB10:0.105017):0.000001):0.007562,C97DCSJFE59:0.112580):0.011703,((C97DCMBS20:0.065542,C97DCMBTB3:0.065542):0.019087,C97DCMBS33:0.084628):0.039654):0.006187):0.005444,(C97DCMBS80:0.114630,C97DCMBTB13:0.114630):0.021282):0.056420,(((F97DCF1EQS16:0.131458,((F97DCF1KP35:0.068281,((F97DCF1KP40:0.054440,F97DCF1KTB136:0.054440):0.007403,F97DCF1KTB50:0.061843):0.006438):0.027048,((F97DCF1KS50:0.079898,F97DCF1KTB165:0.079898):0.008707,F97DCF1MBFE183:0.088605):0.006724):0.036129):0.033308,(((((K97DCEQTB43:0.092859,K97DCKTB160:0.092859):0.006717,(K97DCKP13:0.083167,K97DCKTB111:0.083167):0.016410):0.014149,K97DCMBFE71:0.113728):0.006534,K97DCKTB1:0.120261):0.010952,U97DCKTB17:0.131213):0.033553):0.013338,U97DCEQS8:0.178107):0.014226):0.012566,(((((((G97DCKCC1:0.123110,(((G97DCKFE181:0.085712,G97DCKTB56:0.085712):0.021918,(G97DCKFE77:0.095370,G97DCKP74:0.095370):0.012260):0.011021,((((G97DCKMST100:0.084544,G97DCKMST85:0.084544):0.009980,G97DCMBTB7:0.094524):0.002757,G97DCKS4:0.097281):0.014591,(G97DCKTB142:0.092882,G97DCKTB18:0.092882):0.018988):0.006781):0.004459):0.005898,(((G97DCKMST10:0.084568,G97DCKS30:0.084568):0.015160,G97DCMBFE91:0.099729):0.008825,G97DCKS27:0.108553):0.020456):0.021182,U97DCKTB22:0.150192):0.016657,U97DCKMST135:0.166847):0.009855,U97DCEQS29:0.176702):0.002466,((((J97DCKFE339:0.095333,J97DCMBTB4:0.095333):0.027238,(((J97DCKS22:0.087519,J97DCMBS41:0.087519):0.016195,J97DCKTB147:0.103713):0.013596,J97DCKTB14:0.117310):0.005262):0.020483,J97DCKS16:0.143056):0.012649,U97DCKMST120:0.155705):0.023463):0.025732,(((H97DCEQTB1:0.130368,(H97DCEQTB80:0.130368,(((H97DCKP63:0.106197,H97DCKTB158:0.106197):0.012343,H97DCKS18:0.118539):0.009461,(H97DCKS42:0.114776,H97DCKTB176:0.114776):0.013225):0.002367):0.000001):0.009940,H97DCKTB62:0.140307):0.006118,(((H97DCKCD2:0.096561,(H97DCKMST43:0.088784,(H97DCKTB140:0.078438,H97DCKTB188:0.078438):0.010346):0.007777):0.006028,H97DCKS38:0.102590):0.010076,((H97DCKS43:0.095068,H97DCKTB32:0.095068):0.014928,H97DCKTB52:0.109996):0.002670):0.033759):0.058474):0.000001):0.004212);"
    interval     size
1        193 0.021163
2        192 0.028658
3        191 0.000237
4        190 0.004382
5        189 0.003138
6        188 0.000046
7        187 0.000956
8        186 0.000754
9        185 0.000394
10       184 0.002115
11       183 0.001170
12       182 0.002138
13       181 0.000391
14       180 0.002226
15       179 0.000478
16       178 0.000035
17       177 0.001063
18       176 0.000289
19       175 0.000093
20       174 0.000406
21       173 0.000374
22       172 0.000894
23       171 0.005766
24       170 0.000608
25       169 0.000313
26       168 0.000351
27       167 0.000051
28       166 0.001306
29       165 0.000103
30       164 0.000196
31       163 0.000114
32       162 0.000699
33       161 0.000014
34       160 0.000002
35       159 0.000340
36       158 0.000467
37       157 0.000706
38       156 0.000001
39       155 0.000281
40       154 0.000405
41       153 0.000044
42       152 0.000269
43       151 0.000381
44       150 0.000727
45       149 0.000024
46       148 0.000061
47       147 0.001083
48       146 0.000291
49       145 0.001460
50       144 0.000056
51       143 0.000268
52       142 0.000818
53       141 0.000041
54       140 0.000138
55       139 0.000037
56       138 0.000397
57       137 0.000262
58       136 0.000060
59       135 0.000699
60       134 0.000008
61       133 0.000332
62       132 0.000197
63       131 0.000641
64       130 0.000158
65       129 0.000722
66       128 0.000562
67       127 0.000023
68       126 0.000893
69       125 0.000232
70       124 0.000122
71       123 0.000045
72       122 0.000212
73       121 0.000138
74       120 0.000158
75       119 0.000070
76       118 0.000316
77       117 0.000040
78       116 0.000221
79       115 0.000004
80       114 0.000037
81       113 0.000795
82       112 0.000105
83       111 0.000162
84       110 0.000129
85       109 0.000588
86       108 0.000132
87       107 0.000065
88       106 0.000001
89       105 0.002039
90       104 0.000083
91       103 0.000108
92       102 0.000152
93       101 0.000221
94       100 0.001135
95        99 0.000794
96        98 0.000013
97        97 0.000069
98        96 0.000001
99        95 0.000439
100       94 0.000189
101       93 0.000468
102       92 0.000656
103       91 0.000163
104       90 0.000052
105       89 0.000456
106       88 0.000100
107       87 0.000206
108       86 0.000328
109       85 0.000001
110       84 0.000001
111       83 0.000162
112       82 0.000872
113       81 0.000142
114       80 0.000869
115       79 0.000222
116       78 0.000342
117       77 0.000699
118       76 0.000225
119       75 0.000149
120       74 0.000632
121       73 0.000661
122       72 0.001551
123       71 0.000325
124       70 0.000710
125       69 0.000084
126       68 0.000656
127       67 0.000343
128       66 0.000001
129       65 0.000062
130       64 0.000260
131       63 0.000149
132       62 0.000257
133       61 0.000169
134       60 0.000067
135       59 0.000146
136       58 0.001228
137       57 0.000108
138       56 0.001083
139       55 0.000115
140       54 0.000206
141       53 0.000214
142       52 0.000810
143       51 0.000113
144       50 0.000129
145       49 0.000211
146       48 0.000090
147       47 0.001179
148       46 0.000149
149       45 0.000080
150       44 0.000006
151       43 0.001562
152       42 0.000365
153       41 0.000148
154       40 0.000540
155       39 0.001173
156       38 0.000955
157       37 0.002667
158       36 0.000001
159       35 0.000001
160       34 0.000092
161       33 0.001009
162       32 0.001358
163       31 0.000001
164       30 0.000103
165       29 0.000742
166       28 0.000244
167       27 0.000833
168       26 0.002804
169       25 0.000700
170       24 0.000005
171       23 0.000116
172       22 0.004393
173       21 0.002747
174       20 0.001338
175       19 0.002033
176       18 0.001904
177       17 0.001861
178       16 0.001175
179       15 0.004338
180       14 0.009062
181       13 0.001534
182       12 0.000548
183       11 0.009855
184       10 0.001403
185        9 0.001063
186        8 0.002169
187        7 0.010997
188        6 0.004668
189        5 0.000001
190        4 0.007897
191        3 0.000001
192        2 0.004214
$lineages
  [1] 193 192 191 190 189 188 187 186 185 184 183 182 181 180 179 178 177 176
 [19] 175 174 173 172 171 170 169 168 167 166 165 164 163 162 161 160 159 158
 [37] 157 156 155 154 153 152 151 150 149 148 147 146 145 144 143 142 141 140
 [55] 139 138 137 136 135 134 133 132 131 130 129 128 127 126 125 124 123 122
 [73] 121 120 119 118 117 116 115 114 113 112 111 110 109 108 107 106 105 104
 [91] 103 102 101 100  99  98  97  96  95  94  93  92  91  90  89  88  87  86
[109]  85  84  83  82  81  80  79  78  77  76  75  74  73  72  71  70  69  68
[127]  67  66  65  64  63  62  61  60  59  58  57  56  55  54  53  52  51  50
[145]  49  48  47  46  45  44  43  42  41  40  39  38  37  36  35  34  33  32
[163]  31  30  29  28  27  26  25  24  23  22  21  20  19  18  17  16  15  14
[181]  13  12  11  10   9   8   7   6   5   4   3   2

$interval.length
  [1] 0.021163 0.028658 0.000237 0.004382 0.003138 0.000046 0.000956 0.000754
  [9] 0.000394 0.002115 0.001170 0.002138 0.000391 0.002226 0.000478 0.000035
 [17] 0.001063 0.000289 0.000093 0.000406 0.000374 0.000894 0.005766 0.000608
 [25] 0.000313 0.000351 0.000051 0.001306 0.000103 0.000196 0.000114 0.000699
 [33] 0.000014 0.000002 0.000340 0.000467 0.000706 0.000001 0.000281 0.000405
 [41] 0.000044 0.000269 0.000381 0.000727 0.000024 0.000061 0.001083 0.000291
 [49] 0.001460 0.000056 0.000268 0.000818 0.000041 0.000138 0.000037 0.000397
 [57] 0.000262 0.000060 0.000699 0.000008 0.000332 0.000197 0.000641 0.000158
 [65] 0.000722 0.000562 0.000023 0.000893 0.000232 0.000122 0.000045 0.000212
 [73] 0.000138 0.000158 0.000070 0.000316 0.000040 0.000221 0.000004 0.000037
 [81] 0.000795 0.000105 0.000162 0.000129 0.000588 0.000132 0.000065 0.000001
 [89] 0.002039 0.000083 0.000108 0.000152 0.000221 0.001135 0.000794 0.000013
 [97] 0.000069 0.000001 0.000439 0.000189 0.000468 0.000656 0.000163 0.000052
[105] 0.000456 0.000100 0.000206 0.000328 0.000001 0.000001 0.000162 0.000872
[113] 0.000142 0.000869 0.000222 0.000342 0.000699 0.000225 0.000149 0.000632
[121] 0.000661 0.001551 0.000325 0.000710 0.000084 0.000656 0.000343 0.000001
[129] 0.000062 0.000260 0.000149 0.000257 0.000169 0.000067 0.000146 0.001228
[137] 0.000108 0.001083 0.000115 0.000206 0.000214 0.000810 0.000113 0.000129
[145] 0.000211 0.000090 0.001179 0.000149 0.000080 0.000006 0.001562 0.000365
[153] 0.000148 0.000540 0.001173 0.000955 0.002667 0.000001 0.000001 0.000092
[161] 0.001009 0.001358 0.000001 0.000103 0.000742 0.000244 0.000833 0.002804
[169] 0.000700 0.000005 0.000116 0.004393 0.002747 0.001338 0.002033 0.001904
[177] 0.001861 0.001175 0.004338 0.009062 0.001534 0.000548 0.009855 0.001403
[185] 0.001063 0.002169 0.010997 0.004668 0.000001 0.007897 0.000001 0.004214

$interval.count
[1] 192

$total.depth
[1] 0.209117

attr(,"class")
[1] "coalescentIntervals"

ape documentation built on Sept. 24, 2018, 9:03 a.m.