annotate test-data/files/clsReps.aln.iqtree @ 0:9a3a2e04f47a draft default tip

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author dave
date Mon, 10 Jun 2019 16:04:10 -0400
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1 IQ-TREE 1.6.10 built Mar 21 2019
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2
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3 Input file name: clsReps.aln
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4 Type of analysis: tree reconstruction
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5 Random seed number: 50990
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6
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7 REFERENCES
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8 ----------
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9
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10 To cite IQ-TREE please use:
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11
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12 Lam-Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler, and Bui Quang Minh
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13 (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating
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14 maximum likelihood phylogenies. Mol Biol Evol, 32:268-274.
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15 https://doi.org/10.1093/molbev/msu300
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16
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17 SEQUENCE ALIGNMENT
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18 ------------------
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19
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20 Input data: 84 sequences with 305 nucleotide sites
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21 Number of constant sites: 15 (= 4.91803% of all sites)
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22 Number of invariant (constant or ambiguous constant) sites: 15 (= 4.91803% of all sites)
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23 Number of parsimony informative sites: 238
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24 Number of distinct site patterns: 301
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25
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26 SUBSTITUTION PROCESS
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27 --------------------
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28
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29 Model of substitution: GTR+F+R4
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30
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31 Rate parameter R:
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32
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33 A-C: 1.1368
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34 A-G: 3.5229
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35 A-T: 0.7423
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36 C-G: 0.8278
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37 C-T: 3.3869
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38 G-T: 1.0000
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39
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40 State frequencies: (empirical counts from alignment)
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41
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42 pi(A) = 0.2808
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43 pi(C) = 0.2221
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44 pi(G) = 0.2104
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45 pi(T) = 0.2866
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46
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47 Rate matrix Q:
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48
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49 A -0.9231 0.1932 0.5671 0.1628
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50 C 0.2443 -1.12 0.1333 0.7428
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51 G 0.757 0.1407 -1.117 0.2193
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52 T 0.1595 0.5757 0.161 -0.8962
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53
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54 Model of rate heterogeneity: FreeRate with 4 categories
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55 Site proportion and rates: (0.05215,0.2261) (0.3403,0.5166) (0.301,0.5167) (0.3066,2.143)
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56
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57 Category Relative_rate Proportion
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58 1 0.2261 0.05215
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59 2 0.5166 0.3403
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60 3 0.5167 0.301
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61 4 2.143 0.3066
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62
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63 MAXIMUM LIKELIHOOD TREE
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64 -----------------------
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65
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66 Log-likelihood of the tree: -6705.2658 (s.e. 288.4958)
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67 Unconstrained log-likelihood (without tree): -1739.1499
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68 Number of free parameters (#branches + #model parameters): 179
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69 Akaike information criterion (AIC) score: 13768.5317
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70 Corrected Akaike information criterion (AICc) score: 14284.0517
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71 Bayesian information criterion (BIC) score: 14434.4675
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72
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73 Total tree length (sum of branch lengths): 81.5600
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74 Sum of internal branch lengths: 34.1477 (41.8682% of tree length)
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75
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76 WARNING: 8 near-zero internal branches (<0.0033) should be treated with caution
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77 Such branches are denoted by '**' in the figure below
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78
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79 NOTE: Tree is UNROOTED although outgroup taxon 'K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0' is drawn at root
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80
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81 +--K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0
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82 |
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83 | +**K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1
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84 | +--|
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85 | | +--K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23
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86 | +------|
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87 | | | +-----K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8
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88 | | +----|
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89 | | | +**K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26
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90 | | +---|
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91 | | +--K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51
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92 | +**|
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93 | | | +**K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3
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94 | | | +--|
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95 | | | | +--K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30
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96 | | | +---|
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97 | | | | | +------------K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13
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98 | | | | +--|
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99 | | | | +--K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59
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100 | | | +--|
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101 | | | | | +--K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15
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102 | | | | +-----|
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103 | | | | +--K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33
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104 | | +--|
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105 | | | +**K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52
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106 | | +--|
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107 | | +--K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67
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108 | +--|
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109 | | | +-------K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17
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110 | | +------|
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111 | | | +-----------K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38
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112 | | +--|
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113 | | | +--K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61
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114 | | +--|
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115 | | | +----------------K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77
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116 | | +---|
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117 | | +---K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83
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118 | +--|
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119 | | | +-----K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54
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120 | | +--|
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121 | | +----K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58
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122 | +--|
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123 | | +-------K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32
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124 | +**|
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125 | | | +----------------K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4
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126 | | | +---------|
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127 | | | | +----K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29
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128 | | | +--|
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129 | | | | +--K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25
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130 | | | +---|
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131 | | | | | +--K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11
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132 | | | | +**|
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133 | | | | +--------K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28
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134 | | +**|
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135 | | +--------K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42
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136 | +---|
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137 | | | +--K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45
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138 | | | +--|
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139 | | | | +--K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64
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140 | | +---------------|
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141 | | +**K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49
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142 | +--|
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143 | | | +**K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2
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144 | | | +-------|
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145 | | | | +**K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55
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146 | | | +----|
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147 | | | | +-----K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68
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148 | | | +**|
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149 | | | | +-----------K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70
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150 | | | +--|
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151 | | | | +--K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80
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152 | | | +--|
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153 | | | | | +--K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16
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154 | | | | | +--|
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155 | | | | | | +-----------K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48
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156 | | | | +--|
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157 | | | | | +------------------K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18
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158 | | | | | +--|
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159 | | | | | | +**K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82
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160 | | | | +--------------|
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161 | | | | +**K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21
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162 | | | +--|
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163 | | | | | +-----K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43
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164 | | | | +--|
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165 | | | | | +--K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50
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166 | | | | | +--------|
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167 | | | | | | +**K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63
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168 | | | | +--|
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169 | | | | +--K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53
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parents:
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170 | | | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
171 | | | | | +--K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
172 | | | | +-----|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
173 | | | | | +**K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
174 | | | | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
175 | | | | +--K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
176 | | | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
177 | | | | | +------------K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
178 | | | | | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
179 | | | | | | +-------K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
180 | | | | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
181 | | | | | +**K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
182 | | | | +-----|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
183 | | | | +--K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
184 | | +**|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
185 | | | +--K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
186 | | | +---|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
187 | | | | | +-------------K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
188 | | | | | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
189 | | | | | | +-------K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
190 | | | | | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
191 | | | | | | +---------------K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
192 | | | | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
193 | | | | | +**K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
194 | | | | +------|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
195 | | | | +--K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
196 | | | +-------|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
197 | | | | | +--K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
198 | | | | | +-------|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
199 | | | | | | +**K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
200 | | | | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
201 | | | | | +--K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
202 | | | | +-------|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
203 | | | | +**K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
204 | | | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
205 | | | | +**K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
206 | | +--------|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
207 | | +-------K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
208 | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
209 | | +--K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
210 | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
211 | | | +**K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
212 | | | +**|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
213 | | | | +**K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
214 | | | +----|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
215 | | | | | +-----------K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
216 | | | | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
217 | | | | | +**K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
218 | | | | +---------|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
219 | | | | +--------------K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
220 | | | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
221 | | | | +**K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
222 | | | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
223 | | | | +----K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
224 | | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
225 | | | +--K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
226 | | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
227 | | +**K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
228 | +----|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
229 | | +---------K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
230 | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
231 | | | +-------K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
232 | | +-------|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
233 | | +----K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
234 +**|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
235 | | +**K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
236 | | +-------|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
237 | | | +----------------K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
238 | | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
239 | | | | +------------------K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
240 | | | +----|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
241 | | | +---K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
242 | | +------|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
243 | | | +-------K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
244 | +--|
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
245 | +--------------------K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
246 |
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
247 +**K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
248
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
249 Tree in newick format:
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
250
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
251 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253 TIME STAMP
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254 ----------
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256 Date and time: Tue May 28 13:11:57 2019
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257 Total CPU time used: 115.545 seconds (0h:1m:55s)
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258 Total wall-clock time used: 120.015 seconds (0h:2m:0s)
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