Mercurial > repos > iuc > graphlan_annotate

view test-data/intermediary_tree @ 1:cf1df6b2220a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit b5bd1ab6e4f3a14819dbc2bdad33006bc6131b3c"
author iuc
date Fri, 24 Jan 2020 16:25:56 -0500
parents 5d6f8f0bef7c
children
line wrap: on
line source

<phyloxml xmlns="http://www.phyloxml.org" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd">
  <phylogeny rooted="true">
    <clade>
      <clade>
        <name>k__Archaea</name>
        <branch_length>1.0</branch_length>
        <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.0748302504</property>
        <clade>
          <name>p__Euryarchaeota</name>
          <branch_length>1.0</branch_length>
          <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.0748302504</property>
          <clade>
            <name>c__Methanobacteria</name>
            <branch_length>1.0</branch_length>
            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.0748302504</property>
            <clade>
              <name>o__Methanobacteriales</name>
              <branch_length>1.0</branch_length>
              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.0748302504</property>
              <clade>
                <name>f__Methanobacteriaceae</name>
                <branch_length>1.0</branch_length>
                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.0748302504</property>
                <clade>
                  <name>g__Methanobrevibacter</name>
                  <branch_length>1.0</branch_length>
                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.0748302504</property>
                  <clade>
                    <name>s__Methanobrevibacter_smithii</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.0748302504</property>
                    <clade>
                      <name>t__Methanobrevibacter_smithii_unclassified</name>
                      <branch_length>1.0</branch_length>
                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.0748302504</property>
                    </clade>
                  </clade>
                </clade>
              </clade>
            </clade>
          </clade>
        </clade>
      </clade>
      <clade>
        <name>k__Bacteria</name>
        <branch_length>1.0</branch_length>
        <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">200.0</property>
        <clade>
          <name>p__Actinobacteria</name>
          <branch_length>1.0</branch_length>
          <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.66961905</property>
          <clade>
            <name>c__Actinobacteria</name>
            <branch_length>1.0</branch_length>
            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.66961905</property>
            <clade>
              <name>o__Actinomycetales</name>
              <branch_length>1.0</branch_length>
              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.66961905</property>
              <clade>
                <name>f__Propionibacteriaceae</name>
                <branch_length>1.0</branch_length>
                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.66961905</property>
                <clade>
                  <name>g__Propionibacterium</name>
                  <branch_length>1.0</branch_length>
                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.66961905</property>
                  <clade>
                    <name>s__Propionibacterium_acnes</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.66961905</property>
                    <clade>
                      <name>t__Propionibacterium_acnes_unclassified</name>
                      <branch_length>1.0</branch_length>
                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.66961905</property>
                    </clade>
                  </clade>
                </clade>
              </clade>
            </clade>
          </clade>
        </clade>
        <clade>
          <name>p__Deinococcus_Thermus</name>
          <branch_length>1.0</branch_length>
          <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.298886707</property>
          <clade>
            <name>c__Deinococci</name>
            <branch_length>1.0</branch_length>
            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.298886707</property>
            <clade>
              <name>o__Deinococcales</name>
              <branch_length>1.0</branch_length>
              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.298886707</property>
              <clade>
                <name>f__Deinococcaceae</name>
                <branch_length>1.0</branch_length>
                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.298886707</property>
                <clade>
                  <name>g__Deinococcus</name>
                  <branch_length>1.0</branch_length>
                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.298886707</property>
                  <clade>
                    <name>s__Deinococcus_radiodurans</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">21.1340492974</property>
                    <clade>
                      <name>t__GCF_000008565</name>
                      <branch_length>1.0</branch_length>
                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">21.1340492974</property>
                    </clade>
                  </clade>
                  <clade>
                    <name>s__Deinococcus_unclassified</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">21.1817307606</property>
                  </clade>
                </clade>
              </clade>
            </clade>
          </clade>
        </clade>
        <clade>
          <name>p__Firmicutes</name>
          <branch_length>1.0</branch_length>
          <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">183.285013514</property>
          <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
          <clade>
            <name>c__Bacilli</name>
            <branch_length>1.0</branch_length>
            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">182.398015269</property>
            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
            <clade>
              <name>o__Bacillales</name>
              <branch_length>1.0</branch_length>
              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">164.332515943</property>
              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
              <clade>
                <name>f__Staphylococcaceae</name>
                <branch_length>1.0</branch_length>
                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">164.332515943</property>
                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
                <clade>
                  <name>g__Staphylococcus</name>
                  <branch_length>1.0</branch_length>
                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">164.332515943</property>
                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
                  <clade>
                    <name>s__Staphylococcus_aureus</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">122.793996615</property>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
                    <clade>
                      <name>t__Staphylococcus_aureus_unclassified</name>
                      <branch_length>1.0</branch_length>
                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">122.793996615</property>
                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
                    </clade>
                  </clade>
                  <clade>
                    <name>s__Staphylococcus_epidermidis</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">120.392106048</property>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
                    <clade>
                      <name>t__Staphylococcus_epidermidis_unclassified</name>
                      <branch_length>1.0</branch_length>
                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">120.392106048</property>
                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
                    </clade>
                  </clade>
                </clade>
              </clade>
            </clade>
            <clade>
              <name>o__Lactobacillales</name>
              <branch_length>1.0</branch_length>
              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">96.1062970373</property>
              <clade>
                <name>f__Streptococcaceae</name>
                <branch_length>1.0</branch_length>
                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">96.1062970373</property>
                <clade>
                  <name>g__Streptococcus</name>
                  <branch_length>1.0</branch_length>
                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">96.1062970373</property>
                  <clade>
                    <name>s__Streptococcus_agalactiae</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">25.9449465996</property>
                    <clade>
                      <name>t__Streptococcus_agalactiae_unclassified</name>
                      <branch_length>1.0</branch_length>
                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">25.9449465996</property>
                    </clade>
                  </clade>
                  <clade>
                    <name>s__Streptococcus_mutans</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">93.7375603</property>
                    <clade>
                      <name>t__Streptococcus_mutans_unclassified</name>
                      <branch_length>1.0</branch_length>
                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">93.7375603</property>
                    </clade>
                  </clade>
                </clade>
              </clade>
            </clade>
          </clade>
          <clade>
            <name>c__Clostridia</name>
            <branch_length>1.0</branch_length>
            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property>
            <clade>
              <name>o__Clostridiales</name>
              <branch_length>1.0</branch_length>
              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property>
              <clade>
                <name>f__Clostridiaceae</name>
                <branch_length>1.0</branch_length>
                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property>
                <clade>
                  <name>g__Clostridium</name>
                  <branch_length>1.0</branch_length>
                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property>
                  <clade>
                    <name>s__Clostridium_beijerinckii</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property>
                    <clade>
                      <name>t__Clostridium_beijerinckii_unclassified</name>
                      <branch_length>1.0</branch_length>
                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property>
                    </clade>
                  </clade>
                </clade>
              </clade>
            </clade>
          </clade>
        </clade>
        <clade>
          <name>p__Proteobacteria</name>
          <branch_length>1.0</branch_length>
          <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">102.159086265</property>
          <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#29cc36</property>
          <clade>
            <name>c__Alphaproteobacteria</name>
            <branch_length>1.0</branch_length>
            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">53.6955516997</property>
            <clade>
              <name>o__Rhodobacterales</name>
              <branch_length>1.0</branch_length>
              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">53.6955516997</property>
              <clade>
                <name>f__Rhodobacteraceae</name>
                <branch_length>1.0</branch_length>
                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">53.6955516997</property>
                <clade>
                  <name>g__Rhodobacter</name>
                  <branch_length>1.0</branch_length>
                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">53.6955516997</property>
                  <clade>
                    <name>s__Rhodobacter_sphaeroides</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">53.6955516997</property>
                    <clade>
                      <name>t__Rhodobacter_sphaeroides_unclassified</name>
                      <branch_length>1.0</branch_length>
                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">53.6955516997</property>
                    </clade>
                  </clade>
                </clade>
              </clade>
            </clade>
          </clade>
          <clade>
            <name>c__Betaproteobacteria</name>
            <branch_length>1.0</branch_length>
            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.3264778878</property>
            <clade>
              <name>o__Neisseriales</name>
              <branch_length>1.0</branch_length>
              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.3264778878</property>
              <clade>
                <name>f__Neisseriaceae</name>
                <branch_length>1.0</branch_length>
                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.3264778878</property>
                <clade>
                  <name>g__Neisseria</name>
                  <branch_length>1.0</branch_length>
                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.3264778878</property>
                  <clade>
                    <name>s__Neisseria_meningitidis</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.3264778878</property>
                    <clade>
                      <name>t__Neisseria_meningitidis_unclassified</name>
                      <branch_length>1.0</branch_length>
                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.3264778878</property>
                    </clade>
                  </clade>
                </clade>
              </clade>
            </clade>
          </clade>
          <clade>
            <name>c__Epsilonproteobacteria</name>
            <branch_length>1.0</branch_length>
            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.5761787104</property>
            <clade>
              <name>o__Campylobacterales</name>
              <branch_length>1.0</branch_length>
              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.5761787104</property>
              <clade>
                <name>f__Helicobacteraceae</name>
                <branch_length>1.0</branch_length>
                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.5761787104</property>
                <clade>
                  <name>g__Helicobacter</name>
                  <branch_length>1.0</branch_length>
                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.5761787104</property>
                  <clade>
                    <name>s__Helicobacter_pylori</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.5761787104</property>
                    <clade>
                      <name>t__Helicobacter_pylori_unclassified</name>
                      <branch_length>1.0</branch_length>
                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.5761787104</property>
                    </clade>
                  </clade>
                </clade>
              </clade>
            </clade>
          </clade>
          <clade>
            <name>c__Gammaproteobacteria</name>
            <branch_length>1.0</branch_length>
            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">85.4517057547</property>
            <clade>
              <name>o__Enterobacteriales</name>
              <branch_length>1.0</branch_length>
              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">78.466031643</property>
              <clade>
                <name>f__Enterobacteriaceae</name>
                <branch_length>1.0</branch_length>
                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">78.466031643</property>
                <clade>
                  <name>g__Escherichia</name>
                  <branch_length>1.0</branch_length>
                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">78.466031643</property>
                  <clade>
                    <name>s__Escherichia_coli</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.9341374431</property>
                    <clade>
                      <name>t__Escherichia_coli_unclassified</name>
                      <branch_length>1.0</branch_length>
                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.9341374431</property>
                    </clade>
                  </clade>
                  <clade>
                    <name>s__Escherichia_unclassified</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">49.960616022</property>
                  </clade>
                </clade>
              </clade>
            </clade>
            <clade>
              <name>o__Pseudomonadales</name>
              <branch_length>1.0</branch_length>
              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">34.0879564025</property>
              <clade>
                <name>f__Moraxellaceae</name>
                <branch_length>1.0</branch_length>
                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.9013800671</property>
                <clade>
                  <name>g__Acinetobacter</name>
                  <branch_length>1.0</branch_length>
                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.9013800671</property>
                  <clade>
                    <name>s__Acinetobacter_baumannii</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.9013800671</property>
                    <clade>
                      <name>t__Acinetobacter_baumannii_unclassified</name>
                      <branch_length>1.0</branch_length>
                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.9013800671</property>
                    </clade>
                  </clade>
                </clade>
              </clade>
              <clade>
                <name>f__Pseudomonadaceae</name>
                <branch_length>1.0</branch_length>
                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">33.3271759768</property>
                <clade>
                  <name>g__Pseudomonas</name>
                  <branch_length>1.0</branch_length>
                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">33.3271759768</property>
                  <clade>
                    <name>s__Pseudomonas_aeruginosa</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">25.8720239085</property>
                    <clade>
                      <name>t__Pseudomonas_aeruginosa_unclassified</name>
                      <branch_length>1.0</branch_length>
                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">25.8720239085</property>
                    </clade>
                  </clade>
                  <clade>
                    <name>s__Pseudomonas_unclassified</name>
                    <branch_length>1.0</branch_length>
                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">28.0078913105</property>
                  </clade>
                </clade>
              </clade>
            </clade>
          </clade>
        </clade>
      </clade>
    </clade>
    <property applies_to="phylogeny" datatype="xsd:string" id_ref="class_legend_marker_size" ref="A:1">1.5</property>
    <property applies_to="phylogeny" datatype="xsd:string" id_ref="class_legend_font_size" ref="A:1">10</property>
    <property applies_to="phylogeny" datatype="xsd:string" id_ref="branch_bracket_depth" ref="A:1">0.8</property>
    <property applies_to="phylogeny" datatype="xsd:string" id_ref="clade_separation" ref="A:1">0.5</property>
    <property applies_to="phylogeny" datatype="xsd:string" id_ref="branch_bracket_width" ref="A:1">0.2</property>
    <property applies_to="phylogeny" datatype="xsd:string" id_ref="annotation_legend_font_size" ref="A:1">10</property>
    <property applies_to="phylogeny" datatype="xsd:string" id_ref="leg_keys" ref="A:1">FIRMICUTES_._._PROTEOBACTERIA</property>
    <property applies_to="phylogeny" datatype="xsd:string" id_ref="leg_annotation_background_color" ref="A:1">._._._.</property>
    <property applies_to="phylogeny" datatype="xsd:string" id_ref="leg_annotation_background_edge_color" ref="A:1">._._._.</property>
    <property applies_to="phylogeny" datatype="xsd:string" id_ref="leg_clade_marker_color" ref="A:1">#2d19ff_._._#29cc36</property>
    <property applies_to="phylogeny" datatype="xsd:string" id_ref="leg_clade_marker_edge_width" ref="A:1">._._._.</property>
    <property applies_to="phylogeny" datatype="xsd:string" id_ref="leg_clade_marker_size" ref="A:1">40_._._40</property>
    <property applies_to="phylogeny" datatype="xsd:string" id_ref="leg_clade_marker_shape" ref="A:1">._._._.</property>
    <property applies_to="phylogeny" datatype="xsd:string" id_ref="ignore_branch_len" ref="A:1">1</property>
  </phylogeny>
</phyloxml>