imported>Gydbwiki: New page: {{CAARD |pin_output= (HIV-1:0.240948,(HIV-2:0.242190,SIVMAC:0.024963)N2:0.322066,((SIVMND:0.195084,SIVAGM:0.255789)N4:0.105710,(EIAV:0.495777, (BIV:0.687844,(FIV:0.535661,(VMV:0.195681,(SA...

2009-05-08T11:53:40Z

New page: {{CAARD |pin_output= (HIV-1:0.240948,(HIV-2:0.242190,SIVMAC:0.024963)N2:0.322066,((SIVMND:0.195084,SIVAGM:0.255789)N4:0.105710,(EIAV:0.495777, (BIV:0.687844,(FIV:0.535661,(VMV:0.195681,(SA...

New page

{{CAARD
|pin_output=
(HIV-1:0.240948,(HIV-2:0.242190,SIVMAC:0.024963)N2:0.322066,((SIVMND:0.195084,SIVAGM:0.255789)N4:0.105710,(EIAV:0.495777, (BIV:0.687844,(FIV:0.535661,(VMV:0.195681,(SA-OMVV:0.130900,CAEV:0.176330)N9:0.030231)N8:0.233957)N7:0.158380)N6:0.032682) N5:0.209928)N3:0.023193);

|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>HIV-1</td><td>N1</td><td>0.240948</td><td>-</td></tr><tr><td>HIV-2</td><td>N2</td><td>0.24219</td><td>-</td></tr><tr><td>SIVMAC</td><td>N2</td><td>0.0249634</td><td>-</td></tr><tr><td>SIVMND</td><td>N4</td><td>0.195084</td><td>-</td></tr><tr><td>SIVAGM</td><td>N4</td><td>0.255789</td><td>-</td></tr><tr><td>EIAV</td><td>N5</td><td>0.495777</td><td>-</td></tr><tr><td>BIV</td><td>N6</td><td>0.687844</td><td>-</td></tr><tr><td>FIV</td><td>N7</td><td>0.535661</td><td>-</td></tr><tr><td>VMV</td><td>N8</td><td>0.195681</td><td>-</td></tr><tr><td>SA-OMVV</td><td>N9</td><td>0.1309</td><td>-</td></tr><tr><td>CAEV</td><td>N9</td><td>0.17633</td><td>-</td></tr><tr><td>N1</td><td>root!</td><td>-</td><td>HIV-1 N2 N3</td></tr><tr><td>N2</td><td>N1</td><td>0.322066</td><td>HIV-2 SIVMAC</td></tr><tr><td>N3</td><td>N1</td><td>0.0231928</td><td>N4 N5</td></tr><tr><td>N4</td><td>N3</td><td>0.10571</td><td>SIVMND SIVAGM</td></tr><tr><td>N5</td><td>N3</td><td>0.209928</td><td>EIAV N6</td></tr><tr><td>N6</td><td>N5</td><td>0.0326816</td><td>BIV N7</td></tr><tr><td>N7</td><td>N6</td><td>0.15838</td><td>FIV N8</td></tr><tr><td>N8</td><td>N7</td><td>0.233957</td><td>VMV N9</td></tr><tr><td>N9</td><td>N8</td><td>0.0302306</td><td>SA-OMVV CAEV</td></tr>
</table>

|jpf_output=
<table class="tabdata">
<tbody><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>5.7476e-008</td><td>26</td><td>0.00731698</td><td>52</td><td>4.45852e-008</td><td>78</td><td>8.27202e-007</td></tr><tr class="text"><td>1</td><td>0.000710229</td><td>27</td><td>2.88386e-013</td><td>53</td><td>1.59508e-010</td><td>79</td><td>0.000130151</td></tr><tr class="text"><td>2</td><td>0.000232626</td><td>28</td><td>3.81371e-014</td><td>54</td><td>1.8688e-010</td><td>80</td><td>1.90035e-006</td></tr><tr class="text"><td>3</td><td>0.00475041</td><td>29</td><td>1.31587e-007</td><td>55</td><td>1.64464e-010</td><td>81</td><td>8.33775e-010</td></tr><tr class="text"><td>4</td><td>2.20693e-005</td><td>30</td><td>2.1178e-006</td><td>56</td><td>2.76006e-010</td><td>82</td><td>0.0155517</td></tr><tr class="text"><td>5</td><td>0.000710229</td><td>31</td><td>2.55684e-005</td><td>57</td><td>0.00996842</td><td>83</td><td>1.53987e-006</td></tr><tr class="text"><td>6</td><td>8.43787e-012</td><td>32</td><td>2.04917e-013</td><td>58</td><td>0.00983769</td><td>84</td><td>1.3617e-008</td></tr><tr class="text"><td>7</td><td>4.39935e-007</td><td>33</td><td>6.14377e-010</td><td>59</td><td>0.0138407</td><td>85</td><td>0.00475041</td></tr><tr class="text"><td>8</td><td>6.49805e-006</td><td>34</td><td>2.50307e-009</td><td>60</td><td>5.9434e-009</td><td>86</td><td>0.000726912</td></tr><tr class="text"><td>9</td><td>2.63725e-009</td><td>35</td><td>0.00475041</td><td>61</td><td>2.02065e-010</td><td>87</td><td>1.26968e-006</td></tr><tr class="text"><td>10</td><td>9.04494e-011</td><td>36</td><td>1.43748e-005</td><td>62</td><td>1.23648e-012</td><td>88</td><td>2.2475e-005</td></tr><tr class="text"><td>11</td><td>5.71143e-005</td><td>37</td><td>0.000148363</td><td>63</td><td>3.92614e-011</td><td>89</td><td>3.06924e-008</td></tr><tr class="text"><td>12</td><td>1.79819e-008</td><td>38</td><td>0.0255148</td><td>64</td><td>9.68696e-006</td><td>90</td><td>4.24072e-013</td></tr><tr class="text"><td>13</td><td>2.76373e-015</td><td>39</td><td>0.00475041</td><td>65</td><td>0.000626357</td><td>91</td><td>7.79496e-010</td></tr><tr class="text"><td>14</td><td>5.75746e-018</td><td>40</td><td>0.00818183</td><td>66</td><td>2.01639e-015</td><td>92</td><td>1.22635e-016</td></tr><tr class="text"><td>15</td><td>5.49705e-012</td><td>41</td><td>0.00454973</td><td>67</td><td>1.69588e-015</td><td>93</td><td>1.4552e-008</td></tr><tr class="text"><td>16</td><td>8.4979e-006</td><td>42</td><td>5.56131e-013</td><td>68</td><td>1.40002e-019</td><td>94</td><td>2.65282e-008</td></tr><tr class="text"><td>17</td><td>2.01314e-008</td><td>43</td><td>2.36297e-009</td><td>69</td><td>1.10253e-006</td><td>95</td><td>1.11407e-010</td></tr><tr class="text"><td>18</td><td>9.18525e-007</td><td>44</td><td>7.30644e-011</td><td>70</td><td>4.72957e-009</td><td>96</td><td>4.76167e-014</td></tr><tr class="text"><td>19</td><td>3.99302e-018</td><td>45</td><td>2.49677e-009</td><td>71</td><td>4.79102e-009</td><td>97</td><td>3.78883e-005</td></tr><tr class="text"><td>20</td><td>0.0110107</td><td>46</td><td>6.64372e-009</td><td>72</td><td>1.86631e-008</td><td>98</td><td>1.32658e-007</td></tr><tr class="text"><td>21</td><td>2.7288e-010</td><td>47</td><td>2.00451e-010</td><td>73</td><td>2.5724e-007</td><td>99</td><td>2.59205e-007</td></tr><tr class="text"><td>22</td><td>9.5127e-005</td><td>48</td><td>6.00519e-008</td><td>74</td><td>5.43415e-010</td><td>100</td><td>2.24605e-010</td></tr><tr class="text"><td>23</td><td>3.72236e-016</td><td>49</td><td>1.37822e-011</td><td>75</td><td>1.55809e-013</td><td>101</td><td>1.17443e-010</td></tr><tr class="text"><td>24</td><td>4.24771e-007</td><td>50</td><td>4.20091e-012</td><td>76</td><td>2.18557e-012</td><td>102</td><td>3.52152e-007</td></tr><tr class="text"><td>25</td><td>0.00688408</td><td>51</td><td>0.0101504</td><td>77</td><td>2.8037e-008</td><td> </td><td> </td></tr><tr><td colspan="7" class="grey right">Total log likelihood of joint reconstruction: </td><td class="grey">-1821.38</td></tr>
</table>

|jrof_output=
<align id="lentiviridae" 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>7.69272e-008</td><td>26</td><td>0.053761</td><td>52</td><td>5.02644e-008</td><td>78</td><td>1.22621e-006</td></tr><tr class="text"><td>1</td><td>0.000713303</td><td>27</td><td>7.88163e-013</td><td>53</td><td>4.47837e-010</td><td>79</td><td>0.000130797</td></tr><tr class="text"><td>2</td><td>0.000233367</td><td>28</td><td>2.34587e-013</td><td>54</td><td>5.02691e-010</td><td>80</td><td>4.77703e-006</td></tr><tr class="text"><td>3</td><td>0.00475182</td><td>29</td><td>1.46327e-007</td><td>55</td><td>1.90883e-010</td><td>81</td><td>2.26444e-009</td></tr><tr class="text"><td>4</td><td>2.23371e-005</td><td>30</td><td>3.37457e-006</td><td>56</td><td>3.00782e-010</td><td>82</td><td>0.050901</td></tr><tr class="text"><td>5</td><td>0.000713303</td><td>31</td><td>0.000155734</td><td>57</td><td>0.051691</td><td>83</td><td>3.26661e-006</td></tr><tr class="text"><td>6</td><td>8.87235e-011</td><td>32</td><td>8.45748e-013</td><td>58</td><td>0.051544</td><td>84</td><td>1.81405e-008</td></tr><tr class="text"><td>7</td><td>4.61081e-007</td><td>33</td><td>2.56055e-009</td><td>59</td><td>0.06183</td><td>85</td><td>0.00475182</td></tr><tr class="text"><td>8</td><td>8.17732e-006</td><td>34</td><td>3.69355e-009</td><td>60</td><td>4.57111e-008</td><td>86</td><td>0.000728644</td></tr><tr class="text"><td>9</td><td>4.40838e-009</td><td>35</td><td>0.00475182</td><td>61</td><td>5.06531e-009</td><td>87</td><td>1.86041e-006</td></tr><tr class="text"><td>10</td><td>7.87715e-010</td><td>36</td><td>2.22885e-005</td><td>62</td><td>2.32358e-012</td><td>88</td><td>0.00015284</td></tr><tr class="text"><td>11</td><td>0.000397964</td><td>37</td><td>0.000148594</td><td>63</td><td>4.58417e-011</td><td>89</td><td>4.57224e-008</td></tr><tr class="text"><td>12</td><td>1.47718e-007</td><td>38</td><td>0.073152</td><td>64</td><td>1.52245e-005</td><td>90</td><td>1.15574e-012</td></tr><tr class="text"><td>13</td><td>9.62944e-015</td><td>39</td><td>0.00475182</td><td>65</td><td>0.00297462</td><td>91</td><td>1.16483e-008</td></tr><tr class="text"><td>14</td><td>2.05723e-017</td><td>40</td><td>0.066005</td><td>66</td><td>4.26744e-015</td><td>92</td><td>3.55837e-016</td></tr><tr class="text"><td>15</td><td>1.04797e-011</td><td>41</td><td>0.042645</td><td>67</td><td>5.11101e-015</td><td>93</td><td>1.5565e-008</td></tr><tr class="text"><td>16</td><td>3.93375e-005</td><td>42</td><td>4.39219e-012</td><td>68</td><td>2.18894e-018</td><td>94</td><td>2.70342e-008</td></tr><tr class="text"><td>17</td><td>3.12146e-007</td><td>43</td><td>2.898e-009</td><td>69</td><td>1.1086e-006</td><td>95</td><td>4.74787e-010</td></tr><tr class="text"><td>18</td><td>7.34618e-006</td><td>44</td><td>3.89735e-010</td><td>70</td><td>4.97747e-009</td><td>96</td><td>9.87387e-014</td></tr><tr class="text"><td>19</td><td>5.22933e-017</td><td>45</td><td>5.91622e-009</td><td>71</td><td>2.68439e-008</td><td>97</td><td>7.10306e-005</td></tr><tr class="text"><td>20</td><td>0.032102</td><td>46</td><td>1.38758e-008</td><td>72</td><td>9.93937e-008</td><td>98</td><td>3.65841e-007</td></tr><tr class="text"><td>21</td><td>1.30578e-009</td><td>47</td><td>9.61301e-010</td><td>73</td><td>6.89278e-007</td><td>99</td><td>4.53404e-007</td></tr><tr class="text"><td>22</td><td>9.57315e-005</td><td>48</td><td>6.16114e-008</td><td>74</td><td>1.73143e-009</td><td>100</td><td>3.02339e-010</td></tr><tr class="text"><td>23</td><td>6.40125e-016</td><td>49</td><td>1.76135e-011</td><td>75</td><td>2.94412e-013</td><td>101</td><td>2.74145e-010</td></tr><tr class="text"><td>24</td><td>2.66435e-006</td><td>50</td><td>5.11916e-012</td><td>76</td><td>2.76138e-012</td><td>102</td><td>3.76939e-007</td></tr><tr class="text"><td>25</td><td>0.068765</td><td>51</td><td>0.053761</td><td>77</td><td>2.15765e-007</td><td> </td><td> </td></tr><tr><td colspan="7" class="grey right">Total log likelihood of joint reconstruction: </td><td class="grey">-1720.76</td></tr>
</table>

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

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

|hmms=
<pre>
>AP_lentiviridae profile HMM generated consensus sequence [hmmemit]
LDTGADdtIlkthrdlklpGkpkgkiiiGIGGiikvkkydnVhveikykgkriiGtvvv
vapdtPvnilGRdnmlqkLgirLimaqL
</pre>

|pairwise_alignment=
<pre>
domain 1 of 1, from 1 to 82: score 50.4, E = 6.9e-16

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
+DTGA+ +++++ +kl+ ++P+
AP_lentivi 1 LDTGADD-TILKTH--RDLKLP---------------------GKPK 23

sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
k+ i g+gG+ k+ k++ ++ v+ik + G
AP_lentivi 24 GKI-------IIGIGGIIKV-----KKYDNVH------VEIKYK-G---- 50

venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
+r +++ ++vv p+ + ILGr d + q+ + i+l
AP_lentivi 51 --KRIIGT---VVVV-APDT----PVNILGR-DNMLQKLG--IRL 82
</pre>
}}

CAARD:Lentiviridae - Revision history

imported>Gydbwiki: New page: {{CAARD |pin_output= (HIV-1:0.240948,(HIV-2:0.242190,SIVMAC:0.024963)N2:0.322066,((SIVMND:0.195084,SIVAGM:0.255789)N4:0.105710,(EIAV:0.495777, (BIV:0.687844,(FIV:0.535661,(VMV:0.195681,(SA...