tests...

diff --git a/forester/test_data/clade_analysis_test_1.xml b/forester/test_data/clade_analysis_test_1.xml
new file mode 100644 (file)
index 0000000..1cc6547
--- /dev/null
+++ b/forester/test_data/clade_analysis_test_1.xml
@@ -0,0 +1,127 @@
+<?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/1.20/phyloxml.xsd" xmlns="http://www.phyloxml.org">
+<phylogeny rooted="true" rerootable="true">
+  <clade>
+    <clade>
+      <clade>
+        <clade>
+          <clade>
+            <clade>
+              <name>A.1.1.1</name>
+            </clade>
+            <clade>
+              <name>A.1.1.2</name>
+            </clade>
+            <clade>
+              <name>A.1.1.3</name>
+            </clade>
+            <clade>
+              <clade>
+                <name>A.1.1.4</name>
+              </clade>
+            </clade>
+          </clade>
+          <clade>
+            <name>A.1.2.1</name>
+          </clade>
+        </clade>
+      </clade>
+      <clade>
+        <clade>
+          <clade>
+            <name>A.2.1.1</name>
+          </clade>
+          <clade>
+            <name>A.2.1.2</name>
+          </clade>
+        </clade>
+      </clade>
+      <clade>
+        <clade>
+          <clade>
+            <clade>
+              <clade>
+                <name>A.3.1.1</name>
+              </clade>
+              <clade>
+                <name>A.3.1.2</name>
+              </clade>
+            </clade>
+            <clade>
+              <name>A.3.2.1</name>
+            </clade>
+          </clade>
+          <clade>
+            <name>A.3.3.1</name>
+          </clade>
+        </clade>
+        <clade>
+          <clade>
+            <clade>
+              <name>A.4.1.1</name>
+            </clade>
+            <clade>
+              <name>A.4.1.1.a</name>
+            </clade>
+          </clade>
+          <clade>
+            <clade>
+              <name>A.4.1.2</name>
+            </clade>
+            <clade>
+              <name>A.4.1.2.a</name>
+            </clade>
+          </clade>
+        </clade>
+        <clade>
+          <clade>
+            <name>A.5.1.1</name>
+          </clade>
+          <clade>
+            <name>A.5.1.2</name>
+          </clade>
+        </clade>
+        <clade>
+          <name>A.6.3.12</name>
+        </clade>
+      </clade>
+    </clade>
+    <clade>
+      <clade>
+        <name>B.1.1.1</name>
+      </clade>
+      <clade>
+        <name>B.1.234.3</name>
+      </clade>
+    </clade>
+    <clade>
+      <clade>
+        <clade>
+          <clade>
+            <clade>
+              <clade>
+                <name>C.1.1.1</name>
+              </clade>
+              <clade>
+                <name>C.1.1.2</name>
+              </clade>
+            </clade>
+            <clade>
+              <name>C.1.2.1</name>
+            </clade>
+          </clade>
+          <clade>
+            <name>C.2.1</name>
+          </clade>
+        </clade>
+        <clade>
+          <name>C.3</name>
+        </clade>
+      </clade>
+      <clade>
+        <name>QE.1.1.1.2.1</name>
+      </clade>
+    </clade>
+  </clade>
+</phylogeny>
+</phyloxml>
\ No newline at end of file

diff --git a/forester/test_data/clade_analysis_test_2.xml b/forester/test_data/clade_analysis_test_2.xml
new file mode 100644 (file)
index 0000000..6c1c528
--- /dev/null
+++ b/forester/test_data/clade_analysis_test_2.xml
@@ -0,0 +1,1760 @@
+<?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/1.20/phyloxml.xsd" xmlns="http://www.phyloxml.org">
+<phylogeny rooted="true" rerootable="true">
+  <clade>
+    <clade>
+      <branch_length>0.0285</branch_length>
+      <confidence type="bootstrap">100</confidence>
+      <clade>
+        <branch_length>0.01987</branch_length>
+        <confidence type="bootstrap">65</confidence>
+        <clade>
+          <branch_length>0.03154</branch_length>
+          <confidence type="bootstrap">78</confidence>
+          <clade>
+            <branch_length>0.08356</branch_length>
+            <confidence type="bootstrap">100</confidence>
+            <clade>
+              <branch_length>0.01917</branch_length>
+              <confidence type="bootstrap">66</confidence>
+              <clade>
+                <branch_length>0.02827</branch_length>
+                <confidence type="bootstrap">87</confidence>
+                <clade>
+                  <branch_length>0.0666</branch_length>
+                  <confidence type="bootstrap">100</confidence>
+                  <clade>
+                    <branch_length>0.03294</branch_length>
+                    <confidence type="bootstrap">100</confidence>
+                    <clade>
+                      <branch_length>0.04712</branch_length>
+                      <confidence type="bootstrap">100</confidence>
+                      <clade>
+                        <branch_length>0.0433</branch_length>
+                        <confidence type="bootstrap">100</confidence>
+                        <clade>
+                          <branch_length>0.02052</branch_length>
+                          <confidence type="bootstrap">93</confidence>
+                          <clade>
+                            <branch_length>0.02162</branch_length>
+                            <confidence type="bootstrap">82</confidence>
+                            <clade>
+                              <branch_length>0.06968</branch_length>
+                              <confidence type="bootstrap">100</confidence>
+                              <clade>
+                                <name>6_DQ278891</name>
+                                <branch_length>0.03655</branch_length>
+                              </clade>
+                              <clade>
+                                <name>6_DQ278893</name>
+                                <branch_length>0.03194</branch_length>
+                              </clade>
+                            </clade>
+                            <clade>
+                              <name>6_JX183550</name>
+                              <branch_length>0.09273</branch_length>
+                            </clade>
+                          </clade>
+                          <clade>
+                            <branch_length>0.01616</branch_length>
+                            <confidence type="bootstrap">50</confidence>
+                            <clade>
+                              <branch_length>0.06794</branch_length>
+                              <confidence type="bootstrap">100</confidence>
+                              <clade>
+                                <name>6xb_JX183552</name>
+                                <branch_length>0.04899</branch_length>
+                              </clade>
+                              <clade>
+                                <name>6xb_KJ567645</name>
+                                <branch_length>0.04364</branch_length>
+                              </clade>
+                            </clade>
+                            <clade>
+                              <name>6_JX183551</name>
+                              <branch_length>0.10112</branch_length>
+                            </clade>
+                          </clade>
+                        </clade>
+                        <clade>
+                          <branch_length>0.02796</branch_length>
+                          <confidence type="bootstrap">100</confidence>
+                          <clade>
+                            <name>6_JX183549</name>
+                            <branch_length>0.08974</branch_length>
+                          </clade>
+                          <clade>
+                            <name>6k_D84264</name>
+                            <branch_length>0.08397</branch_length>
+                          </clade>
+                        </clade>
+                      </clade>
+                      <clade>
+                        <branch_length>0.03794</branch_length>
+                        <confidence type="bootstrap">100</confidence>
+                        <clade>
+                          <branch_length>0.03725</branch_length>
+                          <confidence type="bootstrap">100</confidence>
+                          <clade>
+                            <branch_length>0.05687</branch_length>
+                            <confidence type="bootstrap">100</confidence>
+                            <clade>
+                              <name>6l_EF424628</name>
+                              <branch_length>0.02492</branch_length>
+                            </clade>
+                            <clade>
+                              <name>6l_JX183556</name>
+                              <branch_length>0.03726</branch_length>
+                            </clade>
+                          </clade>
+                          <clade>
+                            <name>6_JX183554</name>
+                            <branch_length>0.08936</branch_length>
+                          </clade>
+                        </clade>
+                        <clade>
+                          <name>6_JX183553</name>
+                          <branch_length>0.11203</branch_length>
+                        </clade>
+                      </clade>
+                    </clade>
+                    <clade>
+                      <branch_length>0.04004</branch_length>
+                      <confidence type="bootstrap">100</confidence>
+                      <clade>
+                        <branch_length>0.05084</branch_length>
+                        <confidence type="bootstrap">100</confidence>
+                        <clade>
+                          <branch_length>0.07132</branch_length>
+                          <confidence type="bootstrap">100</confidence>
+                          <clade>
+                            <branch_length>0.00698</branch_length>
+                            <confidence type="bootstrap">54</confidence>
+                            <clade>
+                              <name>6n_DQ278894</name>
+                              <branch_length>0.02024</branch_length>
+                            </clade>
+                            <clade>
+                              <name>6n_EU246938</name>
+                              <branch_length>0.02367</branch_length>
+                            </clade>
+                          </clade>
+                          <clade>
+                            <name>6n_DQ835768</name>
+                            <branch_length>0.02256</branch_length>
+                          </clade>
+                        </clade>
+                        <clade>
+                          <branch_length>0.07615</branch_length>
+                          <confidence type="bootstrap">100</confidence>
+                          <clade>
+                            <name>6xe_JX183557</name>
+                            <branch_length>0.01933</branch_length>
+                          </clade>
+                          <clade>
+                            <name>6xe_km98_KM252792</name>
+                            <branch_length>0.01567</branch_length>
+                          </clade>
+                        </clade>
+                      </clade>
+                      <clade>
+                        <branch_length>0.10494</branch_length>
+                        <confidence type="bootstrap">100</confidence>
+                        <clade>
+                          <name>6m_DQ835766</name>
+                          <branch_length>0.01871</branch_length>
+                        </clade>
+                        <clade>
+                          <name>6m_DQ835767</name>
+                          <branch_length>0.01832</branch_length>
+                        </clade>
+                      </clade>
+                    </clade>
+                  </clade>
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+                    <clade>
+                      <branch_length>0.05365</branch_length>
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+                      <clade>
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+                        <confidence type="bootstrap">100</confidence>
+                        <clade>
+                          <branch_length>0.08105</branch_length>
+                          <confidence type="bootstrap">100</confidence>
+                          <clade>
+                            <name>6j_DQ835761</name>
+                            <branch_length>0.01807</branch_length>
+                          </clade>
+                          <clade>
+                            <name>6j_DQ835769</name>
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+                        </clade>
+                        <clade>
+                          <name>6_JX183558</name>
+                          <branch_length>0.07946</branch_length>
+                        </clade>
+                      </clade>
+                      <clade>
+                        <branch_length>0.08053</branch_length>
+                        <confidence type="bootstrap">100</confidence>
+                        <clade>
+                          <name>6i_DQ835762</name>
+                          <branch_length>0.03111</branch_length>
+                        </clade>
+                        <clade>
+                          <name>6i_DQ835770</name>
+                          <branch_length>0.02</branch_length>
+                        </clade>
+                      </clade>
+                    </clade>
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+                      <branch_length>0.13713</branch_length>
+                    </clade>
+                  </clade>
+                </clade>
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+                  <confidence type="bootstrap">100</confidence>
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+                    <confidence type="bootstrap">100</confidence>
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+                      <branch_length>0.14388</branch_length>
+                      <confidence type="bootstrap">100</confidence>
+                      <clade>
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+                        <confidence type="bootstrap">100</confidence>
+                        <clade>
+                          <name>6xa_EU408330</name>
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+                        </clade>
+                        <clade>
+                          <name>6xa_EU408331</name>
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+                        </clade>
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+                      </clade>
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+                    <confidence type="bootstrap">100</confidence>
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+                      <clade>
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+                      </clade>
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+                <confidence type="bootstrap">100</confidence>
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+                    <confidence type="bootstrap">100</confidence>
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+                      <confidence type="bootstrap">100</confidence>
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+                        <clade>
+                          <name>6xd_L23_KM252789</name>
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+                    <confidence type="bootstrap">100</confidence>
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+                      <clade>
+                        <branch_length>0.00441</branch_length>
+                        <confidence type="bootstrap">100</confidence>
+                        <clade>
+                          <name>6a_AY859526</name>
+                          <branch_length>0.01937</branch_length>
+                        </clade>
+                        <clade>
+                          <name>6a_Y12083</name>
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+                </clade>
+              </clade>
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+            <clade>
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+              <confidence type="bootstrap">100</confidence>
+              <clade>
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+                <confidence type="bootstrap">100</confidence>
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+                    <confidence type="bootstrap">71</confidence>
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+                      <confidence type="bootstrap">95</confidence>
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+                        <confidence type="bootstrap">65</confidence>
+                        <clade>
+                          <branch_length>0.05135</branch_length>
+                          <confidence type="bootstrap">100</confidence>
+                          <clade>
+                            <branch_length>0.03965</branch_length>
+                            <confidence type="bootstrap">100</confidence>
+                            <clade>
+                              <branch_length>0.04734</branch_length>
+                              <confidence type="bootstrap">100</confidence>
+                              <clade>
+                                <branch_length>0.03077</branch_length>
+                                <confidence type="bootstrap">100</confidence>
+                                <clade>
+                                  <name>6e_DQ314805</name>
+                                  <branch_length>0.04758</branch_length>
+                                </clade>
+                                <clade>
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+                                  <branch_length>0.05459</branch_length>
+                                </clade>
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+                              <clade>
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+                      <clade>
+                        <branch_length>0.02414</branch_length>
+                        <confidence type="bootstrap">54</confidence>
+                        <clade>
+                          <branch_length>0.03903</branch_length>
+                          <confidence type="bootstrap">100</confidence>
+                          <clade>
+                            <branch_length>0.09574</branch_length>
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+                            <clade>
+                              <name>6o_EF424627</name>
+                              <branch_length>0.04612</branch_length>
+                            </clade>
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+                            </clade>
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+                            <branch_length>0.12633</branch_length>
+                          </clade>
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+                        <clade>
+                          <branch_length>0.12176</branch_length>
+                          <confidence type="bootstrap">100</confidence>
+                          <clade>
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+                      <confidence type="bootstrap">100</confidence>
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+                    <confidence type="bootstrap">100</confidence>
+                    <clade>
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+                      <confidence type="bootstrap">100</confidence>
+                      <clade>
+                        <name>6f_DQ835760</name>
+                        <branch_length>0.02683</branch_length>
+                      </clade>
+                      <clade>
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+                        <branch_length>0.03064</branch_length>
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+                        <confidence type="bootstrap">100</confidence>
+                        <clade>
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+                        <clade>
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+                        <confidence type="bootstrap">100</confidence>
+                        <clade>
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+                        </clade>
+                        <clade>
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