forester/test_data/clade_analysis_test_2.xml

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.20/phyloxml.xsd" xmlns="http://www.phyloxml.org">
   3 <phylogeny rooted="true" rerootable="true">
   4   <clade>
   5     <clade>
   6       <branch_length>0.0285</branch_length>
   7       <confidence type="bootstrap">100</confidence>
   8       <clade>
   9         <branch_length>0.01987</branch_length>
  10         <confidence type="bootstrap">65</confidence>
  11         <clade>
  12           <branch_length>0.03154</branch_length>
  13           <confidence type="bootstrap">78</confidence>
  14           <clade>
  15             <branch_length>0.08356</branch_length>
  16             <confidence type="bootstrap">100</confidence>
  17             <clade>
  18               <branch_length>0.01917</branch_length>
  19               <confidence type="bootstrap">66</confidence>
  20               <clade>
  21                 <branch_length>0.02827</branch_length>
  22                 <confidence type="bootstrap">87</confidence>
  23                 <clade>
  24                   <branch_length>0.0666</branch_length>
  25                   <confidence type="bootstrap">100</confidence>
  26                   <clade>
  27                     <branch_length>0.03294</branch_length>
  28                     <confidence type="bootstrap">100</confidence>
  29                     <clade>
  30                       <branch_length>0.04712</branch_length>
  31                       <confidence type="bootstrap">100</confidence>
  32                       <clade>
  33                         <branch_length>0.0433</branch_length>
  34                         <confidence type="bootstrap">100</confidence>
  35                         <clade>
  36                           <branch_length>0.02052</branch_length>
  37                           <confidence type="bootstrap">93</confidence>
  38                           <clade>
  39                             <branch_length>0.02162</branch_length>
  40                             <confidence type="bootstrap">82</confidence>
  41                             <clade>
  42                               <branch_length>0.06968</branch_length>
  43                               <confidence type="bootstrap">100</confidence>
  44                               <clade>
  45                                 <name>6_DQ278891</name>
  46                                 <branch_length>0.03655</branch_length>
  47                               </clade>
  48                               <clade>
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  50                                 <branch_length>0.03194</branch_length>
  51                               </clade>
  52                             </clade>
  53                             <clade>
  54                               <name>6_JX183550</name>
  55                               <branch_length>0.09273</branch_length>
  56                             </clade>
  57                           </clade>
  58                           <clade>
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  60                             <confidence type="bootstrap">50</confidence>
  61                             <clade>
  62                               <branch_length>0.06794</branch_length>
  63                               <confidence type="bootstrap">100</confidence>
  64                               <clade>
  65                                 <name>6xb_JX183552</name>
  66                                 <branch_length>0.04899</branch_length>
  67                               </clade>
  68                               <clade>
  69                                 <name>6xb_KJ567645</name>
  70                                 <branch_length>0.04364</branch_length>
  71                               </clade>
  72                             </clade>
  73                             <clade>
  74                               <name>6_JX183551</name>
  75                               <branch_length>0.10112</branch_length>
  76                             </clade>
  77                           </clade>
  78                         </clade>
  79                         <clade>
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  81                           <confidence type="bootstrap">100</confidence>
  82                           <clade>
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  84                             <branch_length>0.08974</branch_length>
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  86                           <clade>
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  94                         <confidence type="bootstrap">100</confidence>
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  97                           <confidence type="bootstrap">100</confidence>
  98                           <clade>
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1113                   <confidence type="bootstrap">100</confidence>
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1136               <clade>
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1138                 <confidence type="bootstrap">100</confidence>
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1245                   <confidence type="bootstrap">100</confidence>
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1258                 <confidence type="bootstrap">100</confidence>
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1261                   <confidence type="bootstrap">100</confidence>
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1264                     <confidence type="bootstrap">100</confidence>
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1267                       <confidence type="bootstrap">62</confidence>
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1301                   <confidence type="bootstrap">91</confidence>
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1304                     <confidence type="bootstrap">66</confidence>
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1307                       <confidence type="bootstrap">78</confidence>
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1310                         <confidence type="bootstrap">100</confidence>
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1313                           <confidence type="bootstrap">100</confidence>
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1319                               <confidence type="bootstrap">100</confidence>
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1322                                 <branch_length>0.00116</branch_length>
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1336                             <branch_length>0.03519</branch_length>
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1344                       <clade>
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1346                         <confidence type="bootstrap">100</confidence>
1347                         <clade>
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1349                           <branch_length>0.07701</branch_length>
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1356                     </clade>
1357                     <clade>
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1362                         <confidence type="bootstrap">100</confidence>
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1377                   </clade>
1378                   <clade>
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1380                     <confidence type="bootstrap">100</confidence>
1381                     <clade>
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1383                       <branch_length>0.06579</branch_length>
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1398                 <confidence type="bootstrap">98</confidence>
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1401                   <confidence type="bootstrap">100</confidence>
1402                   <clade>
1403                     <branch_length>0.02083</branch_length>
1404                     <confidence type="bootstrap">85</confidence>
1405                     <clade>
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1407                       <branch_length>0.03089</branch_length>
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1432     </clade>
1433     <clade>
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1435       <confidence type="bootstrap">100</confidence>
1436       <clade>
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1438         <confidence type="bootstrap">100</confidence>
1439         <clade>
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1441           <confidence type="bootstrap">82</confidence>
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1450                 <confidence type="bootstrap">89</confidence>
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1453                   <confidence type="bootstrap">36</confidence>
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1456                     <confidence type="bootstrap">6</confidence>
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1474                                 <confidence type="bootstrap">83</confidence>
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1477                                   <confidence type="bootstrap">100</confidence>
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1480                                     <branch_length>0.05415</branch_length>
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1492                               <clade>
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1494                                 <confidence type="bootstrap">100</confidence>
1495                                 <clade>
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1502                                 </clade>
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1508                               <clade>
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1514                                 <branch_length>0.08948</branch_length>
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1517                           </clade>
1518                           <clade>
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1520                             <confidence type="bootstrap">19</confidence>
1521                             <clade>
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1523                               <confidence type="bootstrap">75</confidence>
1524                               <clade>
1525                                 <name>2_JF735119</name>
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1530                                 <branch_length>0.09735</branch_length>
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1532                             </clade>
1533                             <clade>
1534                               <branch_length>0.09053</branch_length>
1535                               <confidence type="bootstrap">100</confidence>
1536                               <clade>
1537                                 <name>2m_JF735111</name>
1538                                 <branch_length>0.04172</branch_length>
1539                               </clade>
1540                               <clade>
1541                                 <name>2m_JX227967</name>
1542                                 <branch_length>0.0423</branch_length>
1543                               </clade>
1544                             </clade>
1545                           </clade>
1546                         </clade>
1547                         <clade>
1548                           <branch_length>0.10313</branch_length>
1549                           <confidence type="bootstrap">100</confidence>
1550                           <clade>
1551                             <branch_length>0.03826</branch_length>
1552                             <confidence type="bootstrap">100</confidence>
1553                             <clade>
1554                               <name>2a_AB047639</name>
1555                               <branch_length>0.04646</branch_length>
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1557                             <clade>
1558                               <name>2a_HQ639944</name>
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1565                           </clade>
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1567                       </clade>
1568                       <clade>
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1570                         <confidence type="bootstrap">16</confidence>
1571                         <clade>
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1573                           <confidence type="bootstrap">45</confidence>
1574                           <clade>
1575                             <branch_length>0.06857</branch_length>
1576                             <confidence type="bootstrap">100</confidence>
1577                             <clade>
1578                               <name>2c_D50409</name>
1579                               <branch_length>0.0563</branch_length>
1580                             </clade>
1581                             <clade>
1582                               <name>2c_JX227949</name>
1583                               <branch_length>0.05806</branch_length>
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1585                           </clade>
1586                           <clade>
1587                             <name>2r_JF735115</name>
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1590                         </clade>
1591                         <clade>
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1593                           <confidence type="bootstrap">50</confidence>
1594                           <clade>
1595                             <name>2e_JF735120</name>
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1598                           <clade>
1599                             <name>2i_DQ155561</name>
1600                             <branch_length>0.11756</branch_length>
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1602                         </clade>
1603                       </clade>
1604                     </clade>
1605                     <clade>
1606                       <branch_length>0.00699</branch_length>
1607                       <confidence type="bootstrap">8</confidence>
1608                       <clade>
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1610                         <confidence type="bootstrap">26</confidence>
1611                         <clade>
1612                           <branch_length>0.0249</branch_length>
1613                           <confidence type="bootstrap">33</confidence>
1614                           <clade>
1615                             <branch_length>0.01113</branch_length>
1616                             <confidence type="bootstrap">76</confidence>
1617                             <clade>
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1619                               <confidence type="bootstrap">100</confidence>
1620                               <clade>
1621                                 <name>2f_KC844042</name>
1622                                 <branch_length>0.057</branch_length>
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1625                                 <name>2f_KC844050</name>
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1631                               <branch_length>0.09114</branch_length>
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1634                           <clade>
1635                             <name>2p:L39300_L44601</name>
1636                             <branch_length>0.11287</branch_length>
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1638                         </clade>
1639                         <clade>
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1643                       </clade>
1644                       <clade>
1645                         <branch_length>0.02758</branch_length>
1646                         <confidence type="bootstrap">24</confidence>
1647                         <clade>
1648                           <name>2h:X93327</name>
1649                           <branch_length>0.11698</branch_length>
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1651                         <clade>
1652                           <name>2n:L39309_L44602</name>
1653                           <branch_length>0.13476</branch_length>
1654                         </clade>
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1656                     </clade>
1657                   </clade>
1658                   <clade>
1659                     <branch_length>0.0874</branch_length>
1660                     <confidence type="bootstrap">100</confidence>
1661                     <clade>
1662                       <branch_length>0.01617</branch_length>
1663                       <confidence type="bootstrap">93</confidence>
1664                       <clade>
1665                         <name>2j_HM777358</name>
1666                         <branch_length>0.05378</branch_length>
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1668                       <clade>
1669                         <name>2j_HM777359</name>
1670                         <branch_length>0.04852</branch_length>
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1672                     </clade>
1673                     <clade>
1674                       <name>2j_JF735113</name>
1675                       <branch_length>0.06474</branch_length>
1676                     </clade>
1677                   </clade>
1678                 </clade>
1679                 <clade>
1680                   <name>2o:L38333_L38373</name>
1681                   <branch_length>0.08206</branch_length>
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1683               </clade>
1684               <clade>
1685                 <branch_length>0.05792</branch_length>
1686                 <confidence type="bootstrap">99</confidence>
1687                 <clade>
1688                   <name>2_JF735110</name>
1689                   <branch_length>0.11747</branch_length>
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1691                 <clade>
1692                   <name>2_KC197239</name>
1693                   <branch_length>0.11386</branch_length>
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1696             </clade>
1697             <clade>
1698               <branch_length>0.01986</branch_length>
1699               <confidence type="bootstrap">46</confidence>
1700               <clade>
1701                 <branch_length>0.04088</branch_length>
1702                 <confidence type="bootstrap">99</confidence>
1703                 <clade>
1704                   <branch_length>0.10683</branch_length>
1705                   <confidence type="bootstrap">100</confidence>
1706                   <clade>
1707                     <branch_length>0.01838</branch_length>
1708                     <confidence type="bootstrap">100</confidence>
1709                     <clade>
1710                       <branch_length>0.02008</branch_length>
1711                       <confidence type="bootstrap">100</confidence>
1712                       <clade>
1713                         <name>2b_AB030907</name>
1714                         <branch_length>0.04288</branch_length>
1715                       </clade>
1716                       <clade>
1717                         <name>2b_D10988</name>
1718                         <branch_length>0.03415</branch_length>
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1720                     </clade>
1721                     <clade>
1722                       <name>2b_AB661388</name>
1723                       <branch_length>0.05789</branch_length>
1724                     </clade>
1725                   </clade>
1726                   <clade>
1727                     <name>2b_AB661382</name>
1728                     <branch_length>0.04237</branch_length>
1729                   </clade>
1730                 </clade>
1731                 <clade>
1732                   <name>2t_KC197238</name>
1733                   <branch_length>0.13334</branch_length>
1734                 </clade>
1735               </clade>
1736               <clade>
1737                 <name>2_KC197236</name>
1738                 <branch_length>0.15312</branch_length>
1739               </clade>
1740             </clade>
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1742           <clade>
1743             <name>2_KC197237</name>
1744             <branch_length>0.13399</branch_length>
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1747         <clade>
1748           <name>2s:JQ924942_HM777447_HM777332</name>
1749           <branch_length>0.08823</branch_length>
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1753         <name>7a_EF108306</name>
1754         <branch_length>0.28303</branch_length>
1755       </clade>
1756     </clade>
1757   </clade>
1758 </phylogeny>
1759
1760 </phyloxml>