CAARD:Spumaretroviridae - Revision history

imported>Gydbwiki: New page: {{CAARD |pin_output= (EFV:0.238833,(FFV:0.023485,FSV:0.042109)N2:0.306572,(HFV:0.234101,SFV:0.140934)N3:0.179964); |fin_output=

Name<...
2009-05-08T13:42:16Z

New page: {{CAARD |pin_output= (EFV:0.238833,(FFV:0.023485,FSV:0.042109)N2:0.306572,(HFV:0.234101,SFV:0.140934)N3:0.179964); |fin_output= <table class="tabdata"> <tr class="grey"> <td>Name<...

New page
{{CAARD
|pin_output=
(EFV:0.238833,(FFV:0.023485,FSV:0.042109)N2:0.306572,(HFV:0.234101,SFV:0.140934)N3:0.179964);

|fin_output=
<table class="tabdata">
<tr class="grey">
<td>Name</td>
<td>Father</td>
<td>Distance to father</td>
<td>Sons</td>
</tr>
<tr><td>EFV</td><td>N1</td><td>0.238833</td><td>-</td></tr><tr><td>FFV</td><td>N2</td><td>0.0234848</td><td>-</td></tr><tr><td>FSV</td><td>N2</td><td>0.0421088</td><td>-</td></tr><tr><td>HFV</td><td>N3</td><td>0.234101</td><td>-</td></tr><tr><td>SFV</td><td>N3</td><td>0.140934</td><td>-</td></tr><tr><td>N1</td><td>root!</td><td>-</td><td>EFV N2 N3</td></tr><tr><td>N2</td><td>N1</td><td>0.306572</td><td>FFV FSV</td></tr><tr><td>N3</td><td>N1</td><td>0.179964</td><td>HFV SFV</td></tr>
</table>

|jpf_output=
<table class="tabdata">
<tr class="grey">
<td>Position</td>
<td>Joint probability</td>
<td>Position</td>
<td>Joint probability</td>
<td>Position</td>
<td>Joint probability</td>
<td>Position</td>
<td>Joint probability</td>
</tr>
<tr class="text"><td>0</td><td>5.38165e-005</td><td>36</td><td>0.0163904</td><td>72</td><td>0.000609575</td><td>108</td><td>0.0192524</td></tr><tr class="text"><td>1</td><td>0.0157724</td><td>37</td><td>0.0159724</td><td>73</td><td>5.80535e-007</td><td>109</td><td>9.28822e-009</td></tr><tr class="text"><td>2</td><td>0.000941077</td><td>38</td><td>0.0159724</td><td>74</td><td>8.01854e-005</td><td>110</td><td>0.0210204</td></tr><tr class="text"><td>3</td><td>0.000154035</td><td>39</td><td>4.50382e-005</td><td>75</td><td>0.0427951</td><td>111</td><td>0.0159724</td></tr><tr class="text"><td>4</td><td>0.0185706</td><td>40</td><td>0.000449852</td><td>76</td><td>0.000483347</td><td>112</td><td>8.46963e-006</td></tr><tr class="text"><td>5</td><td>8.28536e-006</td><td>41</td><td>0.00135471</td><td>77</td><td>0.0427951</td><td>113</td><td>1.69495e-006</td></tr><tr class="text"><td>6</td><td>0.000341814</td><td>42</td><td>0.0210204</td><td>78</td><td>0.0127656</td><td>114</td><td>0.0427951</td></tr><tr class="text"><td>7</td><td>0.0127656</td><td>43</td><td>0.00191487</td><td>79</td><td>0.00026707</td><td>115</td><td>0.00990647</td></tr><tr class="text"><td>8</td><td>0.0102574</td><td>44</td><td>6.82761e-006</td><td>80</td><td>6.8191e-005</td><td>116</td><td>0.0122447</td></tr><tr class="text"><td>9</td><td>0.00197487</td><td>45</td><td>0.0346535</td><td>81</td><td>0.000120462</td><td>117</td><td>1.32629e-006</td></tr><tr class="text"><td>10</td><td>0.0219636</td><td>46</td><td>0.0160012</td><td>82</td><td>3.26162e-005</td><td>118</td><td>0.00990647</td></tr><tr class="text"><td>11</td><td>4.30465e-007</td><td>47</td><td>0.00210299</td><td>83</td><td>2.17262e-006</td><td>119</td><td>0.0212073</td></tr><tr class="text"><td>12</td><td>3.19192e-009</td><td>48</td><td>0.000119588</td><td>84</td><td>0.0007896</td><td>120</td><td>0.00982481</td></tr><tr class="text"><td>13</td><td>0.00135471</td><td>49</td><td>5.3135e-006</td><td>85</td><td>0.000563605</td><td>121</td><td>0.0122447</td></tr><tr class="text"><td>14</td><td>0.0427951</td><td>50</td><td>0.00163053</td><td>86</td><td>2.81052e-005</td><td>122</td><td>0.0163904</td></tr><tr class="text"><td>15</td><td>1.96977e-006</td><td>51</td><td>0.0212073</td><td>87</td><td>0.000350486</td><td>123</td><td>0.0346535</td></tr><tr class="text"><td>16</td><td>6.0325e-005</td><td>52</td><td>0.0163904</td><td>88</td><td>1.95868e-006</td><td>124</td><td>0.00617817</td></tr><tr class="text"><td>17</td><td>0.0212073</td><td>53</td><td>0.0128442</td><td>89</td><td>6.54418e-007</td><td>125</td><td>0.0160012</td></tr><tr class="text"><td>18</td><td>2.92775e-006</td><td>54</td><td>4.60951e-005</td><td>90</td><td>0.0012468</td><td>126</td><td>2.30157e-005</td></tr><tr class="text"><td>19</td><td>0.0219636</td><td>55</td><td>0.00074352</td><td>91</td><td>0.0427951</td><td>127</td><td>0.0128442</td></tr><tr class="text"><td>20</td><td>0.0025148</td><td>56</td><td>8.0892e-006</td><td>92</td><td>4.06985e-007</td><td>128</td><td>9.23027e-006</td></tr><tr class="text"><td>21</td><td>3.00009e-005</td><td>57</td><td>7.76743e-005</td><td>93</td><td>2.0497e-007</td><td>129</td><td>0.0219636</td></tr><tr class="text"><td>22</td><td>3.25698e-007</td><td>58</td><td>0.00176538</td><td>94</td><td>0.0013369</td><td>130</td><td>0.00617817</td></tr><tr class="text"><td>23</td><td>8.88376e-008</td><td>59</td><td>0.0159724</td><td>95</td><td>2.83628e-008</td><td>131</td><td>4.70692e-006</td></tr><tr class="text"><td>24</td><td>3.83208e-009</td><td>60</td><td>0.000108371</td><td>96</td><td>0.0427951</td><td>132</td><td>0.0128442</td></tr><tr class="text"><td>25</td><td>0.0025148</td><td>61</td><td>0.000674823</td><td>97</td><td>2.07178e-005</td><td>133</td><td>0.0185706</td></tr><tr class="text"><td>26</td><td>1.20134e-005</td><td>62</td><td>6.75141e-005</td><td>98</td><td>1.34233e-007</td><td>134</td><td>0.0127656</td></tr><tr class="text"><td>27</td><td>0.0127656</td><td>63</td><td>9.33133e-005</td><td>99</td><td>3.39411e-007</td><td>135</td><td>0.0346535</td></tr><tr class="text"><td>28</td><td>0.0128442</td><td>64</td><td>0.0219636</td><td>100</td><td>1.00373e-007</td><td>136</td><td>8.58916e-005</td></tr><tr class="text"><td>29</td><td>0.00617817</td><td>65</td><td>5.27655e-005</td><td>101</td><td>0.0210204</td><td>137</td><td>1.33635e-006</td></tr><tr class="text"><td>30</td><td>0.0346535</td><td>66</td><td>0.0157724</td><td>102</td><td>1.747e-005</td><td>138</td><td>2.20555e-006</td></tr><tr class="text"><td>31</td><td>2.36026e-006</td><td>67</td><td>0.000374918</td><td>103</td><td>5.68067e-008</td><td>139</td><td>0.0219636</td></tr><tr class="text"><td>32</td><td>1.218e-005</td><td>68</td><td>0.0219636</td><td>104</td><td>0.0427951</td><td>140</td><td>2.08666e-005</td></tr><tr class="text"><td>33</td><td>1.747e-005</td><td>69</td><td>0.00990647</td><td>105</td><td>0.000360498</td><td>141</td><td>0.0219636</td></tr><tr class="text"><td>34</td><td>9.93251e-007</td><td>70</td><td>3.99612e-006</td><td>106</td><td>5.89657e-010</td><td> </td><td> </td></tr><tr class="text"><td>35</td><td>6.67866e-008</td><td>71</td><td>2.61721e-007</td><td>107</td><td>0.0427951</td><td> </td><td> </td></tr><tr><td colspan="7" class="grey right">Total log likelihood of joint reconstruction: </td><td class="grey">-1170.16</td></tr>
</table>

|jrof_output=
<align id="spumaretroviridae" folder="jrof"></align>

|mpf_output=
<table class="tabdata">
<tr class="grey">
<td>Position</td>
<td>Joint probability</td>
<td>Position</td>
<td>Joint probability</td>
<td>Position</td>
<td>Joint probability</td>
<td>Position</td>
<td>Joint probability</td>
</tr>
<tr class="text"><td>0</td><td>5.39429e-005</td><td>36</td><td>0.0164673</td><td>72</td><td>0.000624667</td><td>108</td><td>0.0192564</td></tr><tr class="text"><td>1</td><td>0.0158022</td><td>37</td><td>0.0159757</td><td>73</td><td>6.8528e-007</td><td>109</td><td>3.001e-008</td></tr><tr class="text"><td>2</td><td>0.00103337</td><td>38</td><td>0.0159757</td><td>74</td><td>8.133e-005</td><td>110</td><td>0.0210437</td></tr><tr class="text"><td>3</td><td>0.000155907</td><td>39</td><td>6.85118e-005</td><td>75</td><td>0.0428175</td><td>111</td><td>0.0159757</td></tr><tr class="text"><td>4</td><td>0.0186019</td><td>40</td><td>0.0004647</td><td>76</td><td>0.000536886</td><td>112</td><td>1.14869e-005</td></tr><tr class="text"><td>5</td><td>1.94975e-005</td><td>41</td><td>0.00137545</td><td>77</td><td>0.0428175</td><td>113</td><td>3.46889e-006</td></tr><tr class="text"><td>6</td><td>0.000376027</td><td>42</td><td>0.0210437</td><td>78</td><td>0.0127835</td><td>114</td><td>0.0428175</td></tr><tr class="text"><td>7</td><td>0.0127835</td><td>43</td><td>0.00205224</td><td>79</td><td>0.000282481</td><td>115</td><td>0.00990647</td></tr><tr class="text"><td>8</td><td>0.0102575</td><td>44</td><td>7.26115e-006</td><td>80</td><td>7.16352e-005</td><td>116</td><td>0.0122492</td></tr><tr class="text"><td>9</td><td>0.00215097</td><td>45</td><td>0.0346585</td><td>81</td><td>0.000291131</td><td>117</td><td>4.0908e-006</td></tr><tr class="text"><td>10</td><td>0.0219664</td><td>46</td><td>0.016018</td><td>82</td><td>3.41474e-005</td><td>118</td><td>0.00990647</td></tr><tr class="text"><td>11</td><td>1.23857e-006</td><td>47</td><td>0.00222136</td><td>83</td><td>2.33433e-006</td><td>119</td><td>0.0212479</td></tr><tr class="text"><td>12</td><td>5.93373e-009</td><td>48</td><td>0.000248522</td><td>84</td><td>0.000806841</td><td>120</td><td>0.00983248</td></tr><tr class="text"><td>13</td><td>0.00137545</td><td>49</td><td>1.31476e-005</td><td>85</td><td>0.000582907</td><td>121</td><td>0.0122492</td></tr><tr class="text"><td>14</td><td>0.0428175</td><td>50</td><td>0.00172856</td><td>86</td><td>3.01171e-005</td><td>122</td><td>0.0164673</td></tr><tr class="text"><td>15</td><td>3.31103e-006</td><td>51</td><td>0.0212479</td><td>87</td><td>0.000366387</td><td>123</td><td>0.0346585</td></tr><tr class="text"><td>16</td><td>6.95011e-005</td><td>52</td><td>0.0164673</td><td>88</td><td>2.45704e-006</td><td>124</td><td>0.00617957</td></tr><tr class="text"><td>17</td><td>0.0212479</td><td>53</td><td>0.0128941</td><td>89</td><td>2.26225e-006</td><td>125</td><td>0.016018</td></tr><tr class="text"><td>18</td><td>4.55511e-006</td><td>54</td><td>9.71756e-005</td><td>90</td><td>0.0012795</td><td>126</td><td>2.60973e-005</td></tr><tr class="text"><td>19</td><td>0.0219664</td><td>55</td><td>0.000889906</td><td>91</td><td>0.0428175</td><td>127</td><td>0.0128941</td></tr><tr class="text"><td>20</td><td>0.00272774</td><td>56</td><td>1.28445e-005</td><td>92</td><td>7.16817e-007</td><td>128</td><td>1.3172e-005</td></tr><tr class="text"><td>21</td><td>4.91919e-005</td><td>57</td><td>8.27521e-005</td><td>93</td><td>9.80248e-007</td><td>129</td><td>0.0219664</td></tr><tr class="text"><td>22</td><td>1.71897e-006</td><td>58</td><td>0.0018584</td><td>94</td><td>0.00140047</td><td>130</td><td>0.00617957</td></tr><tr class="text"><td>23</td><td>3.20357e-007</td><td>59</td><td>0.0159757</td><td>95</td><td>1.14778e-007</td><td>131</td><td>8.52544e-006</td></tr><tr class="text"><td>24</td><td>1.89377e-008</td><td>60</td><td>0.000163348</td><td>96</td><td>0.0428175</td><td>132</td><td>0.0128941</td></tr><tr class="text"><td>25</td><td>0.00272774</td><td>61</td><td>0.000765705</td><td>97</td><td>4.23819e-005</td><td>133</td><td>0.0186019</td></tr><tr class="text"><td>26</td><td>1.93766e-005</td><td>62</td><td>0.000161294</td><td>98</td><td>5.76599e-007</td><td>134</td><td>0.0127835</td></tr><tr class="text"><td>27</td><td>0.0127835</td><td>63</td><td>0.000244769</td><td>99</td><td>9.28581e-007</td><td>135</td><td>0.0346585</td></tr><tr class="text"><td>28</td><td>0.0128941</td><td>64</td><td>0.0219664</td><td>100</td><td>3.34824e-007</td><td>136</td><td>8.75251e-005</td></tr><tr class="text"><td>29</td><td>0.00617957</td><td>65</td><td>5.81919e-005</td><td>101</td><td>0.0210437</td><td>137</td><td>1.58573e-006</td></tr><tr class="text"><td>30</td><td>0.0346585</td><td>66</td><td>0.0158022</td><td>102</td><td>2.02749e-005</td><td>138</td><td>2.36759e-006</td></tr><tr class="text"><td>31</td><td>4.91344e-006</td><td>67</td><td>0.000571642</td><td>103</td><td>1.28046e-007</td><td>139</td><td>0.0219664</td></tr><tr class="text"><td>32</td><td>1.87707e-005</td><td>68</td><td>0.0219664</td><td>104</td><td>0.0428175</td><td>140</td><td>4.7806e-005</td></tr><tr class="text"><td>33</td><td>2.02749e-005</td><td>69</td><td>0.00990647</td><td>105</td><td>0.000383944</td><td>141</td><td>0.0219664</td></tr><tr class="text"><td>34</td><td>1.18159e-006</td><td>70</td><td>7.50055e-006</td><td>106</td><td>5.32244e-009</td><td> </td><td> </td></tr><tr class="text"><td>35</td><td>1.16635e-007</td><td>71</td><td>3.9184e-007</td><td>107</td><td>0.0428175</td><td> </td><td> </td></tr><tr><td colspan="7" class="grey right">Total log likelihood of joint reconstruction: </td><td class="grey">-1130.91</td></tr>
</table>

|mrof_output=
<align id="spumaretroviridae" folder="mrof"></align>

|sequence_logo=
[[Image:Logo_spumaretroviridae.png|500px|center]]

|hmms=
<pre>
>AP_spumaretroviridae profile HMM generated consensus sequence
wDsgAditCvPksfLeeEePikkrliktiHGekeenvYYltfKiqGRkveaEvigtpld
YvlisPsDiPWllkkpLeLtikvdlqeqqerlLnktiLskegKeqLksLFvKYdnLWqh
WEnqvGHRrirPHkiAtGtvnPrP
</pre>

|pairwise_alignment=
<pre>
Domain 1 of 1, from 1 to 84: score 36.8, E = 8.6e-12

DTG_ILG template ->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
+D+GA++ ++++k+ ++ P+
AP_spumare 1 WDSGADI-TCVPKS--FLEEEE-----------------------PI 21

sktsttaqdtirgagGqs..kiyvSklktsgqirknllslvtikitkGnv
+k+ i++++G++++++y+ l++++q rk v+ ++ G
AP_spumare 22 KKRL------IKTIHGEKeeNVYY--LTFKIQGRK-----VEAEVI-G-- 55

TevenrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-
+++ d +++ +p+d ++++L ++ + +dl
AP_spumare 56 ------TPL-D--YVLI-SPSD----IPWLLKK-PLELTIK---VDL 84
</pre>
}}