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<?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">
<name>example from Prof. Joe Felsenstein's book "Inferring Phylogenies"</name>
<description>phyloXML allows to use either a "branch_length" attribute or element to indicate branch lengths.</description>
<clade>
<clade branch_length="0.06">
<clade branch_length="0.102">
<name>A</name>
</clade>
<clade branch_length="0.23">
<name>B</name>
</clade>
</clade>
<clade branch_length="0.4">
<name>C</name>
</clade>
</clade>
</phylogeny>
<phylogeny rooted="true">
<name>example from Prof. Joe Felsenstein's book "Inferring Phylogenies"</name>
<description>phyloXML allows to use either a "branch_length" attribute or element to indicate branch lengths.</description>
<clade>
<clade>
<branch_length>0.06</branch_length>
<clade>
<name>A</name>
<branch_length>0.102</branch_length>
</clade>
<clade>
<name>B</name>
<branch_length>0.23</branch_length>
</clade>
</clade>
<clade>
<name>C</name>
<branch_length>0.4</branch_length>
</clade>
</clade>
</phylogeny>
<phylogeny rooted="true">
<name>same example, with support of type "bootstrap"</name>
<clade>
<clade branch_length="0.06">
<name>AB</name>
<confidence type="bootstrap">89</confidence>
<clade branch_length="0.102">
<name>A</name>
</clade>
<clade branch_length="0.23">
<name>B</name>
</clade>
</clade>
<clade branch_length="0.4">
<name>C</name>
</clade>
</clade>
</phylogeny>
<phylogeny rooted="true">
<name>same example, with species and sequence</name>
<clade>
<clade>
<name>AB</name>
<clade>
<name>A</name>
<taxonomy>
<scientific_name>E. coli</scientific_name>
</taxonomy>
<sequence>
<annotation>
<desc>alcohol dehydrogenase</desc>
<confidence type="probability">0.99</confidence>
</annotation>
</sequence>
</clade>
<clade>
<name>B</name>
<taxonomy>
<scientific_name>B. subtilis</scientific_name>
</taxonomy>
<sequence>
<annotation>
<desc>alcohol dehydrogenase</desc>
<confidence type="probability">0.91</confidence>
</annotation>
</sequence>
</clade>
</clade>
<clade>
<name>C</name>
<taxonomy>
<scientific_name>C. elegans</scientific_name>
</taxonomy>
<sequence>
<annotation>
<desc>alcohol dehydrogenase</desc>
<confidence type="probability">0.67</confidence>
</annotation>
</sequence>
</clade>
</clade>
</phylogeny>
<phylogeny rooted="true">
<name>same example, with gene duplication information and sequence relationships</name>
<clade>
<events>
<speciations>1</speciations>
</events>
<clade>
<events>
<duplications>1</duplications>
</events>
<clade>
<taxonomy>
<scientific_name>Bacillus subtilis</scientific_name>
</taxonomy>
<sequence id_source="x">
<symbol>adhB</symbol>
<accession source="ncbi">AAB80874</accession>
<name>alcohol dehydrogenase</name>
</sequence>
</clade>
<clade>
<taxonomy>
<scientific_name>Bacillus subtilis</scientific_name>
</taxonomy>
<sequence id_source="y">
<symbol>gbsB</symbol>
<accession source="ncbi">CAB15083</accession>
<name>alcohol dehydrogenase</name>
</sequence>
</clade>
</clade>
<clade>
<taxonomy>
<scientific_name>Caenorhabditis elegans</scientific_name>
</taxonomy>
<sequence id_source="z">
<symbol>ADHX</symbol>
<accession source="ncbi">Q17335</accession>
<name>alcohol dehydrogenase</name>
<annotation ref="InterPro:IPR002085"/>
</sequence>
</clade>
</clade>
<sequence_relation id_ref_0="x" id_ref_1="y" type="paralogy"/>
<sequence_relation id_ref_0="x" id_ref_1="z" type="orthology"/>
<sequence_relation id_ref_0="y" id_ref_1="z" type="orthology"/>
</phylogeny>
<phylogeny rooted="true">
<name>similar example, with more detailed sequence data</name>
<clade>
<clade>
<clade>
<taxonomy>
<id provider="NCBI">6645</id>
<code>OCTVU</code>
<scientific_name>Octopus vulgaris</scientific_name>
</taxonomy>
<sequence>
<symbol>ADHX</symbol>
<accession source="UniProtKB">P81431</accession>
<name>Alcohol dehydrogenase class-3</name>
<mol_seq>TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD</mol_seq>
<annotation ref="EC:1.1.1.1"/>
<annotation ref="GO:0004022"/>
</sequence>
</clade>
<clade>
<taxonomy>
<id provider="NCBI">44689</id>
<code>DICDI</code>
<scientific_name>Dictyostelium discoideum</scientific_name>
</taxonomy>
<sequence>
<symbol>RT4I1</symbol>
<accession source="UniProtKB">Q54II4</accession>
<name>Reticulon-4-interacting protein 1 homolog, mitochondrial precursor</name>
<mol_seq>MKGILLNGYGESLDLLEYKTDLPVPKPIKSQVLIKIHSTSINPLDNVMRK</mol_seq>
<annotation ref="GO:0008270"/>
<annotation ref="GO:0016491"/>
</sequence>
</clade>
</clade>
<clade>
<taxonomy>
<id provider="NCBI">1488</id>
<code>CLOAB</code>
<scientific_name>Clostridium acetobutylicum</scientific_name>
</taxonomy>
<sequence>
<symbol>ADHB</symbol>
<accession source="UniProtKB">Q04945</accession>
<name>NADH-dependent butanol dehydrogenase B</name>
<mol_seq>MVDFEYSIPTRIFFGKDKINVLGRELKKYGSKVLIVYGGGSIKRNGIYDK</mol_seq>
<annotation ref="GO:0046872"/>
<annotation ref="KEGG:Tetrachloroethene degradation"/>
</sequence>
</clade>
</clade>
</phylogeny>
<phylogeny rooted="false">
<name>network, node B is connected to TWO nodes: AB and C</name>
<clade>
<clade id_source="ab" branch_length="0.06">
<name>AB</name>
<clade id_source="a" branch_length="0.102">
<name>A</name>
</clade>
<clade id_source="b" branch_length="0.23">
<name>B</name>
</clade>
</clade>
<clade id_source="c" branch_length="0.4">
<name>C</name>
</clade>
</clade>
<clade_relation id_ref_0="b" id_ref_1="c" type="network_connection"/>
</phylogeny>
<phylogeny rooted="true">
<name>same example, using property elements to indicate a "depth" value for marine organisms</name>
<clade>
<clade>
<name>AB</name>
<clade>
<name>A</name>
<property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 1200 </property>
</clade>
<clade>
<name>B</name>
<property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 2300 </property>
</clade>
</clade>
<clade>
<name>C</name>
<property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 200 </property>
</clade>
</clade>
</phylogeny>
<phylogeny rooted="true">
<name>same example, using property elements to indicate a "depth" value for marine organisms by using id refs in
order to have property elements outside of the tree topology</name>
<clade>
<clade>
<name>AB</name>
<clade id_source="id_a">
<name>A</name>
</clade>
<clade id_source="id_b">
<name>B</name>
</clade>
</clade>
<clade id_source="id_c">
<name>C</name>
</clade>
</clade>
<property id_ref="id_a" datatype="xsd:integer" ref="NOAA:depth" applies_to="node" unit="METRIC:m"> 1200 </property>
<property id_ref="id_b" datatype="xsd:integer" ref="NOAA:depth" applies_to="node" unit="METRIC:m"> 2300 </property>
<property id_ref="id_c" datatype="xsd:integer" ref="NOAA:depth" applies_to="node" unit="METRIC:m"> 200 </property>
</phylogeny>
<phylogeny rooted="true">
<name>monitor lizards</name>
<description>a pylogeny of some monitor lizards</description>
<clade>
<taxonomy>
<id provider="NCBI">8556</id>
<scientific_name>Varanus</scientific_name>
<rank>genus</rank>
<uri desc="EMBL REPTILE DATABASE">http://www.embl-heidelberg.de/~uetz/families/Varanidae.html</uri>
</taxonomy>
<clade>
<taxonomy>
<id provider="NCBI">62046</id>
<scientific_name>Varanus niloticus</scientific_name>
<common_name>Nile monitor</common_name>
<rank>species</rank>
</taxonomy>
<distribution>
<desc>Africa</desc>
</distribution>
</clade>
<clade>
<taxonomy>
<scientific_name>Odatria</scientific_name>
<rank>subgenus</rank>
</taxonomy>
<clade>
<taxonomy>
<id provider="NCBI">169855</id>
<scientific_name>Varanus storri</scientific_name>
<common_name>Storr's monitor</common_name>
<rank>species</rank>
</taxonomy>
<distribution>
<desc>Australia</desc>
</distribution>
</clade>
<clade>
<taxonomy>
<id provider="NCBI">62053</id>
<scientific_name>Varanus timorensis</scientific_name>
<common_name>Timor monitor</common_name>
<rank>species</rank>
</taxonomy>
<distribution>
<desc>Asia</desc>
</distribution>
</clade>
</clade>
</clade>
</phylogeny>
<phylogeny rooted="true">
<name>A tree with phylogeographic information</name>
<clade>
<clade>
<clade>
<name>A</name>
<distribution>
<desc>Hirschweg, Winterthur, Switzerland</desc>
<point geodetic_datum="WGS84">
<lat>47.481277</lat>
<long>8.769303</long>
<alt>472</alt>
</point>
</distribution>
</clade>
<clade>
<name>B</name>
<distribution>
<desc>Nagoya, Aichi, Japan</desc>
<point geodetic_datum="WGS84">
<lat>35.155904</lat>
<long>136.915863</long>
<alt>10</alt>
</point>
</distribution>
</clade>
<clade>
<name>C</name>
<distribution>
<desc>ETH Zürich</desc>
<point geodetic_datum="WGS84">
<lat>47.376334</lat>
<long>8.548108</long>
<alt>452</alt>
</point>
</distribution>
</clade>
</clade>
<clade>
<name>D</name>
<distribution>
<desc>San Diego</desc>
<point geodetic_datum="WGS84">
<lat>32.880933</lat>
<long>-117.217543</long>
<alt>104</alt>
</point>
</distribution>
</clade>
</clade>
</phylogeny>
<phylogeny rooted="true">
<name>A tree with date information</name>
<clade>
<clade>
<clade>
<name>A</name>
<date unit="mya">
<desc>Silurian</desc>
<value>425</value>
<minimum>416.0</minimum>
<maximum>443.7</maximum>
</date>
</clade>
<clade>
<name>B</name>
<date unit="mya">
<desc>Devonian</desc>
<value>320</value>
</date>
</clade>
</clade>
<clade>
<name>C</name>
<date unit="mya">
<desc>Ediacaran</desc>
<value>600</value>
</date>
</clade>
</clade>
</phylogeny>
<phylogeny rooted="true">
<name>Using another XML language to store an alignment</name>
<clade>
<clade>
<clade>
<name>A</name>
</clade>
<clade>
<name>B</name>
</clade>
</clade>
<clade>
<name>C</name>
</clade>
</clade>
</phylogeny>
<align:alignment xmlns:align="http://example.org/align">
<seq name="A">acgtcgcggcccgtggaagtcctctcct</seq>
<seq name="B">aggtcgcggcctgtggaagtcctctcct</seq>
<seq name="C">taaatcgc--cccgtgg-agtccc-cct</seq>
</align:alignment>
</phyloxml>
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