blast
authorcmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Fri, 5 Oct 2012 20:04:53 +0000 (20:04 +0000)
committercmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Fri, 5 Oct 2012 20:04:53 +0000 (20:04 +0000)
forester/aptx/aptx_example_files/BLAST_examples.xml [new file with mode: 0644]

diff --git a/forester/aptx/aptx_example_files/BLAST_examples.xml b/forester/aptx/aptx_example_files/BLAST_examples.xml
new file mode 100644 (file)
index 0000000..27096be
--- /dev/null
@@ -0,0 +1,951 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" xmlns="http://www.phyloxml.org">
+<phylogeny rooted="true">
+  <clade>
+    <events>
+      <duplications>1</duplications>
+    </events>
+    <clade>
+      <branch_length>0.100405</branch_length>
+      <confidence type="unknown">100</confidence>
+      <events>
+        <duplications>1</duplications>
+      </events>
+      <clade>
+        <branch_length>0.41517</branch_length>
+        <confidence type="unknown">100</confidence>
+        <events>
+          <duplications>1</duplications>
+        </events>
+        <clade>
+          <branch_length>0.30159</branch_length>
+          <confidence type="unknown">97</confidence>
+          <events>
+            <duplications>1</duplications>
+          </events>
+          <clade>
+            <branch_length>0.15021</branch_length>
+            <confidence type="unknown">69</confidence>
+            <events>
+              <duplications>1</duplications>
+            </events>
+            <clade>
+              <branch_length>0.04885</branch_length>
+              <confidence type="unknown">68</confidence>
+              <events>
+                <speciations>1</speciations>
+              </events>
+              <clade>
+                <branch_length>0.04633</branch_length>
+                <confidence type="unknown">59</confidence>
+                <events>
+                  <speciations>1</speciations>
+                </events>
+                <clade>
+                  <branch_length>0.18918</branch_length>
+                  <confidence type="unknown">100</confidence>
+                  <events>
+                    <speciations>1</speciations>
+                  </events>
+                  <clade>
+                    <branch_length>0.07518</branch_length>
+                    <confidence type="unknown">97</confidence>
+                    <events>
+                      <speciations>1</speciations>
+                    </events>
+                    <clade>
+                      <branch_length>0.0073</branch_length>
+                      <confidence type="unknown">100</confidence>
+                      <events>
+                        <speciations>1</speciations>
+                      </events>
+                      <clade>
+                        <branch_length>0.0036</branch_length>
+                        <confidence type="unknown">91</confidence>
+                        <events>
+                          <speciations>1</speciations>
+                        </events>
+                        <clade>
+                          <name>NP_001025424.1</name>
+                          <branch_length>1.0E-5</branch_length>
+                          <taxonomy>
+                            <scientific_name>Danio rerio</scientific_name>
+                          </taxonomy>
+                        </clade>
+                        <clade>
+                          <branch_length>0.00327</branch_length>
+                          <taxonomy>
+                            <scientific_name>Felis catus</scientific_name>
+                          </taxonomy>
+                          <sequence>
+                            <accession source="ncbi">ABJ16409.1</accession>
+                            <name>BCL2</name>
+                          </sequence>
+                        </clade>
+                      </clade>
+                      <clade>
+                        <name>hsCLCN7</name>
+                        <branch_length>0.00962</branch_length>
+                        <taxonomy>
+                          <scientific_name>HUMAN</scientific_name>
+                        </taxonomy>
+                      </clade>
+                    </clade>
+                    <clade>
+                      <name>ggClcn7</name>
+                      <branch_length>0.28745</branch_length>
+                      <taxonomy>
+                        <scientific_name>CHICK</scientific_name>
+                      </taxonomy>
+                    </clade>
+                  </clade>
+                  <clade>
+                    <name>frClcn_g150497</name>
+                    <branch_length>0.12824</branch_length>
+                    <taxonomy>
+                      <scientific_name>FUGRU</scientific_name>
+                    </taxonomy>
+                  </clade>
+                </clade>
+                <clade>
+                  <name>ciClc_146907</name>
+                  <branch_length>0.38499</branch_length>
+                  <taxonomy>
+                    <scientific_name>CIOIN</scientific_name>
+                  </taxonomy>
+                </clade>
+              </clade>
+              <clade>
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+                <confidence type="unknown">100</confidence>
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+                <clade>
+                  <name>dmClc_CG8594</name>
+                  <branch_length>0.29315</branch_length>
+                  <taxonomy>
+                    <scientific_name>DROME</scientific_name>
+                  </taxonomy>
+                </clade>
+                <clade>
+                  <name>agClc_g16563</name>
+                  <branch_length>0.18816</branch_length>
+                  <taxonomy>
+                    <scientific_name>ANOGA</scientific_name>
+                  </taxonomy>
+                </clade>
+              </clade>
+            </clade>
+            <clade>
+              <branch_length>0.4337</branch_length>
+              <confidence type="unknown">100</confidence>
+              <events>
+                <speciations>1</speciations>
+              </events>
+              <clade>
+                <name>cbClcn_CBG23365</name>
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+                <taxonomy>
+                  <scientific_name>CAEBR</scientific_name>
+                </taxonomy>
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+                <name>ceClcn_CE29336</name>
+                <branch_length>0.00466</branch_length>
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+                </taxonomy>
+              </clade>
+            </clade>
+          </clade>
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+            <branch_length>0.27675</branch_length>
+            <confidence type="unknown">100</confidence>
+            <events>
+              <speciations>1</speciations>
+            </events>
+            <clade>
+              <branch_length>0.16193</branch_length>
+              <confidence type="unknown">100</confidence>
+              <events>
+                <speciations>1</speciations>
+              </events>
+              <clade>
+                <branch_length>0.06936</branch_length>
+                <confidence type="unknown">98</confidence>
+                <events>
+                  <speciations>1</speciations>
+                </events>
+                <clade>
+                  <branch_length>0.03192</branch_length>
+                  <confidence type="unknown">100</confidence>
+                  <events>
+                    <speciations>1</speciations>
+                  </events>
+                  <clade>
+                    <branch_length>0.02482</branch_length>
+                    <confidence type="unknown">99</confidence>
+                    <events>
+                      <speciations>1</speciations>
+                    </events>
+                    <clade>
+                      <name>rnClcn6</name>
+                      <branch_length>0.01157</branch_length>
+                      <taxonomy>
+                        <scientific_name>RAT</scientific_name>
+                      </taxonomy>
+                    </clade>
+                    <clade>
+                      <name>mmClcn6</name>
+                      <branch_length>0.00537</branch_length>
+                      <taxonomy>
+                        <scientific_name>MOUSE</scientific_name>
+                      </taxonomy>
+                    </clade>
+                  </clade>
+                  <clade>
+                    <name>hsCLCN6</name>
+                    <branch_length>0.00234</branch_length>
+                    <taxonomy>
+                      <scientific_name>HUMAN</scientific_name>
+                    </taxonomy>
+                  </clade>
+                </clade>
+                <clade>
+                  <name>ggClcn6</name>
+                  <branch_length>0.08378</branch_length>
+                  <taxonomy>
+                    <scientific_name>CHICK</scientific_name>
+                  </taxonomy>
+                </clade>
+              </clade>
+              <clade>
+                <name>frClcn_g153343</name>
+                <branch_length>0.23936</branch_length>
+                <taxonomy>
+                  <scientific_name>FUGRU</scientific_name>
+                </taxonomy>
+              </clade>
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+              <name>ciClc_139586</name>
+              <branch_length>0.35537</branch_length>
+              <taxonomy>
+                <scientific_name>CIOIN</scientific_name>
+              </taxonomy>
+            </clade>
+          </clade>
+        </clade>
+        <clade>
+          <branch_length>0.37011</branch_length>
+          <confidence type="unknown">100</confidence>
+          <events>
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+          </events>
+          <clade>
+            <name>ciClc_145284</name>
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+            <taxonomy>
+              <scientific_name>CIOIN</scientific_name>
+            </taxonomy>
+          </clade>
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+            <name>ggClcn_nov1</name>
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+            <taxonomy>
+              <scientific_name>CHICK</scientific_name>
+            </taxonomy>
+          </clade>
+        </clade>
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+        <branch_length>0.42764</branch_length>
+        <confidence type="unknown">100</confidence>
+        <events>
+          <duplications>1</duplications>
+        </events>
+        <clade>
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+          <confidence type="unknown">91</confidence>
+          <events>
+            <speciations>1</speciations>
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+              <confidence type="unknown">100</confidence>
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+                <confidence type="unknown">67</confidence>
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+                </events>
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+                  <confidence type="unknown">97</confidence>
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+                  </events>
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+                    <confidence type="unknown">86</confidence>
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+                      <speciations>1</speciations>
+                    </events>
+                    <clade>
+                      <branch_length>0.04239</branch_length>
+                      <confidence type="unknown">100</confidence>
+                      <events>
+                        <speciations>1</speciations>
+                      </events>
+                      <clade>
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+                        <confidence type="unknown">97</confidence>
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+                          <speciations>1</speciations>
+                        </events>
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+                          <name>rnClcn5</name>
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+                            <scientific_name>RAT</scientific_name>
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+                        </clade>
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+                          <branch_length>1.0E-5</branch_length>
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+                        <name>hsCLCN4</name>
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+                          <scientific_name>HUMAN</scientific_name>
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+                        <scientific_name>CHICK</scientific_name>
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+                <clade>
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+                    <speciations>1</speciations>
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+                        <speciations>1</speciations>
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+                        <scientific_name>MOUSE</scientific_name>
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+                    <name>ggClcn3</name>
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+                  <name>frClcn_g127864</name>
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+            <clade>
+              <name>agClc_g16174</name>
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+                <scientific_name>ANOGA</scientific_name>
+              </taxonomy>
+            </clade>
+            <clade>
+              <name>dmClc_CG5284</name>
+              <branch_length>0.16939</branch_length>
+              <taxonomy>
+                <scientific_name>DROME</scientific_name>
+              </taxonomy>
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+          </clade>
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+          <branch_length>0.30137</branch_length>
+          <confidence type="unknown">100</confidence>
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+          <clade>
+            <name>cbClcn_CBG03262</name>
+            <branch_length>1.0E-5</branch_length>
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+              <scientific_name>CAEBR</scientific_name>
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+            <taxonomy>
+              <scientific_name>CAEEL</scientific_name>
+            </taxonomy>
+          </clade>
+        </clade>
+      </clade>
+    </clade>
+    <clade>
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+      <confidence type="unknown">100</confidence>
+      <events>
+        <duplications>1</duplications>
+      </events>
+      <clade>
+        <branch_length>0.15381</branch_length>
+        <confidence type="unknown">64</confidence>
+        <events>
+          <duplications>1</duplications>
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+        <clade>
+          <branch_length>0.03139</branch_length>
+          <confidence type="unknown">59</confidence>
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+            <speciations>1</speciations>
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+          <clade>
+            <branch_length>0.09003</branch_length>
+            <confidence type="unknown">77</confidence>
+            <events>
+              <speciations>1</speciations>
+            </events>
+            <clade>
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+              <confidence type="unknown">100</confidence>
+              <events>
+                <duplications>1</duplications>
+              </events>
+              <clade>
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+    </clade>
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+</phylogeny>
+</phyloxml>
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