<?xml version="1.0" encoding="utf-8"?>
<orthoXML xmlns="http://orthoXML.org/2011/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="0.3" origin="InParanoid" originVersion="8.0" xsi:schemaLocation="http://orthoXML.org/2011/ http://www.orthoxml.org/0.3/orthoxml.xsd">
  <notes>
    <stats ortholog_groups="3139" inparalogs="9015"/>
    <parameters scoreCutoff="40" confidenceCutoff="0.05" overlapCutoff="0.5" mergingCutoff="0.5" matrix="BLOSUM62"/>
  </notes>
  <species name="Caenorhabditis brenneri " NCBITaxId="135651">
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        <gene id="8899" protId="G0N3N4" geneId="CAEBREN_03198"/>
        <gene id="8900" protId="G0PEX4" geneId="CAEBREN_03992"/>
        <gene id="8901" protId="G0NC46" geneId="CAEBREN_15225"/>
        <gene id="8902" protId="G0PNG5" geneId="CAEBREN_22452"/>
        <gene id="8903" protId="G0NBA8" geneId="CAEBREN_17412"/>
        <gene id="8904" protId="G0N7X1" geneId="CAEBREN_11034"/>
        <gene id="8905" protId="G0PGL2" geneId="CAEBREN_20315"/>
        <gene id="8906" protId="G0NIV9" geneId="CAEBREN_14033"/>
        <gene id="8907" protId="G0PHR5" geneId="CAEBREN_12031"/>
        <gene id="8908" protId="G0MJ24" geneId="CAEBREN_15969"/>
        <gene id="8909" protId="G0MLL4" geneId="CAEBREN_23892"/>
        <gene id="8910" protId="G0PK83" geneId="CAEBREN_19303"/>
        <gene id="8911" protId="G0PJC5" geneId="CAEBREN_19628"/>
        <gene id="8912" protId="G0NY63" geneId="CAEBREN_12804"/>
        <gene id="8920" protId="G0NVJ9" geneId="CAEBREN_08575"/>
        <gene id="8921" protId="G0PG29" geneId="CAEBREN_13109"/>
        <gene id="8923" protId="G0NQC9" geneId="Cbn-glb-14"/>
        <gene id="8924" protId="G0N6T6" geneId="CAEBREN_23182"/>
        <gene id="8926" protId="G0PGV6" geneId="CAEBREN_07487"/>
        <gene id="8927" protId="G0NK71" geneId="CAEBREN_13516"/>
        <gene id="8929" protId="G0M6Q0" geneId="CAEBREN_15176"/>
        <gene id="8931" protId="G0NAC2" geneId="Cbn-jtr-1"/>
        <gene id="8933" protId="G0MUV0" geneId="Cbn-tag-281"/>
        <gene id="8935" protId="G0MFT1" geneId="Cbn-stn-1"/>
        <gene id="8936" protId="G0PCU6" geneId="CAEBREN_29873"/>
        <gene id="8939" protId="G0MI83" geneId="CAEBREN_30781"/>
        <gene id="8940" protId="G0PHE6" geneId="CAEBREN_09596"/>
        <gene id="8942" protId="G0NRB2" geneId="CAEBREN_29032"/>
        <gene id="8943" protId="G0NRB4" geneId="CAEBREN_19089"/>
        <gene id="8945" protId="G0MKW4" geneId="CAEBREN_17231"/>
        <gene id="8947" protId="G0P2N9" geneId="Cbn-lpd-8"/>
        <gene id="8949" protId="G0PM84" geneId="CAEBREN_02621"/>
        <gene id="8951" protId="G0PI14" geneId="CAEBREN_10014"/>
        <gene id="8955" protId="G0NLF2" geneId="Cbn-cps-6"/>
        <gene id="8956" protId="G0NQ03" geneId="CAEBREN_29353"/>
        <gene id="8958" protId="G0NR50" geneId="CAEBREN_10640"/>
        <gene id="8959" protId="G0N3T7" geneId="CAEBREN_18783"/>
        <gene id="8961" protId="G0MGB3" geneId="CAEBREN_16498"/>
        <gene id="8963" protId="G0P972" geneId="CAEBREN_29751"/>
        <gene id="8965" protId="G0MH21" geneId="Cbn-dyf-7"/>
        <gene id="8981" protId="G0MXC0" geneId="Cbn-glb-13"/>
        <gene id="8985" protId="G0N5I7" geneId="CAEBREN_06784"/>
        <gene id="8987" protId="G0NQY9" geneId="CAEBREN_28773"/>
        <gene id="8989" protId="G0N427" geneId="Cbn-ctg-2"/>
        <gene id="8990" protId="G0M7Q5" geneId="Cbn-cgr-1"/>
        <gene id="8991" protId="G0MRT5" geneId="CAEBREN_00109"/>
        <gene id="8992" protId="G0P307" geneId="CAEBREN_26403"/>
        <gene id="8993" protId="G0PGQ9" geneId="CAEBREN_16655"/>
        <gene id="8994" protId="G0PDC7" geneId="CAEBREN_29474"/>
        <gene id="8995" protId="G0NR77" geneId="CAEBREN_24802"/>
        <gene id="9002" protId="G0NVH3" geneId="CAEBREN_29074"/>
        <gene id="9003" protId="G0NH69" geneId="CAEBREN_00131"/>
        <gene id="9004" protId="G0NH70" geneId="CAEBREN_23998"/>
        <gene id="9006" protId="G0PMX9" geneId="CAEBREN_31612"/>
        <gene id="9007" protId="G0N7E9" geneId="Cbn-oig-1"/>
        <gene id="9009" protId="G0MLC8" geneId="CAEBREN_16579"/>
        <gene id="9011" protId="G0NRX3" geneId="CAEBREN_17693"/>
        <gene id="9012" protId="G0NLY4" geneId="CAEBREN_03210"/>
        <gene id="9013" protId="G0NZV5" geneId="CAEBREN_31453"/>
        <gene id="9014" protId="G0NZV4" geneId="CAEBREN_17510"/>
      </genes>
    </database>
    <notes>
      <additionalInformation abbreviation="C.brenneri" link="http://www.uniprot.org/taxonomy/135651"/>
    </notes>
  </species>
  <species name="Ciona savignyi " NCBITaxId="51511">
    <database name="UniProt" version="UniProt_Complete_Proteomes_2013_06" protLink="http://www.uniprot.org/uniprot/">
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        <gene id="8490" protId="H2ZMC0" geneId="Csa.4923"/>
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        <gene id="8499" protId="H2YEJ8" geneId="uncharacterized_H2YEJ8"/>
        <gene id="8502" protId="H2ZFF4" geneId="Csa.3539"/>
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        <gene id="8511" protId="H2ZI60" geneId="uncharacterized_H2ZI60"/>
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        <gene id="8522" protId="H2YQ53" geneId="uncharacterized_H2YQ53"/>
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        <gene id="8524" protId="H2ZCQ0" geneId="uncharacterized_H2ZCQ0"/>
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        <gene id="8558" protId="H2Y464" geneId="uncharacterized_H2Y464"/>
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        <gene id="8562" protId="H2YNV8" geneId="Csa.5982"/>
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        <gene id="8574" protId="H2Z6F3" geneId="uncharacterized_H2Z6F3"/>
        <gene id="8577" protId="H2Y8Z1" geneId="Csa.9833"/>
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        <gene id="8581" protId="H2ZFX4" geneId="Csa.5805"/>
        <gene id="8583" protId="H2YYQ8" geneId="uncharacterized_H2YYQ8"/>
        <gene id="8641" protId="H2YTY2" geneId="uncharacterized_H2YTY2"/>
        <gene id="8642" protId="H2YTW6" geneId="uncharacterized_H2YTW6"/>
        <gene id="8643" protId="H2YTZ4" geneId="uncharacterized_H2YTZ4"/>
        <gene id="8645" protId="H2YBT3" geneId="uncharacterized_H2YBT3"/>
        <gene id="8646" protId="H2YBS8" geneId="Csa.10285"/>
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        <gene id="8651" protId="H2Y5A8" geneId="uncharacterized_H2Y5A8"/>
        <gene id="8663" protId="H2ZMM4" geneId="uncharacterized_H2ZMM4"/>
        <gene id="8664" protId="H2Z9Y6" geneId="uncharacterized_H2Z9Y6"/>
        <gene id="8665" protId="H2YVM7" geneId="uncharacterized_H2YVM7"/>
        <gene id="8666" protId="H2Z6A4" geneId="uncharacterized_H2Z6A4"/>
        <gene id="8671" protId="H2Z514" geneId="uncharacterized_H2Z514"/>
        <gene id="8672" protId="H2ZPK6" geneId="uncharacterized_H2ZPK6"/>
        <gene id="8673" protId="H2ZCL9" geneId="Csa.6403"/>
        <gene id="8674" protId="H2ZPK7" geneId="uncharacterized_H2ZPK7"/>
        <gene id="8676" protId="H2YG91" geneId="Csa.5565"/>
        <gene id="8678" protId="H2Y4M5" geneId="uncharacterized_H2Y4M5"/>
        <gene id="8680" protId="H2Y9H4" geneId="uncharacterized_H2Y9H4"/>
        <gene id="8683" protId="H2Z462" geneId="Csa.7988"/>
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        <gene id="8688" protId="H2ZP97" geneId="uncharacterized_H2ZP97"/>
        <gene id="8690" protId="H2YMJ5" geneId="uncharacterized_H2YMJ5"/>
        <gene id="8694" protId="H2YRZ6" geneId="uncharacterized_H2YRZ6"/>
        <gene id="8695" protId="H2Z7I6" geneId="uncharacterized_H2Z7I6"/>
        <gene id="8696" protId="H2ZMU2" geneId="uncharacterized_H2ZMU2"/>
        <gene id="8697" protId="H2ZLY4" geneId="uncharacterized_H2ZLY4"/>
        <gene id="8701" protId="H2ZNF0" geneId="uncharacterized_H2ZNF0"/>
        <gene id="8704" protId="H2YJI3" geneId="Csa.4985"/>
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        <gene id="8708" protId="H2YCA0" geneId="Csa.10333"/>
        <gene id="8710" protId="H2YNI7" geneId="uncharacterized_H2YNI7"/>
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        <gene id="8714" protId="H2Z439" geneId="uncharacterized_H2Z439"/>
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        <gene id="8718" protId="H2YX31" geneId="Csa.6379"/>
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        <gene id="8720" protId="H2Z0R4" geneId="uncharacterized_H2Z0R4"/>
        <gene id="8721" protId="H2YPM5" geneId="uncharacterized_H2YPM5"/>
        <gene id="8726" protId="H2ZA78" geneId="uncharacterized_H2ZA78"/>
        <gene id="8727" protId="H2ZA77" geneId="uncharacterized_H2ZA77"/>
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        <gene id="8729" protId="H2ZGW3" geneId="Csa.9377"/>
        <gene id="8730" protId="H2YKV7" geneId="uncharacterized_H2YKV7"/>
        <gene id="8733" protId="H2ZB06" geneId="uncharacterized_H2ZB06"/>
        <gene id="8734" protId="H2Y7S8" geneId="uncharacterized_H2Y7S8"/>
        <gene id="8737" protId="H2ZPS7" geneId="uncharacterized_H2ZPS7"/>
        <gene id="8738" protId="H2YYA4" geneId="Csa.9299"/>
        <gene id="8740" protId="H2YCR7" geneId="uncharacterized_H2YCR7"/>
        <gene id="8742" protId="H2Z8B7" geneId="Csa.5820"/>
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        <gene id="8751" protId="H2ZAX1" geneId="Csa.1135"/>
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        <gene id="8753" protId="H2ZP91" geneId="Csa.4373"/>
        <gene id="8762" protId="H2YQG9" geneId="uncharacterized_H2YQG9"/>
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        <gene id="8775" protId="H2ZF38" geneId="uncharacterized_H2ZF38"/>
        <gene id="8779" protId="H2Z6H8" geneId="Csa.5542"/>
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        <gene id="8785" protId="Q9XY06" geneId="CsEndo-3"/>
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        <gene id="8788" protId="H2YL05" geneId="uncharacterized_H2YL05"/>
        <gene id="8791" protId="H2ZMY5" geneId="Csa.2928"/>
        <gene id="8793" protId="H2Y8U4" geneId="uncharacterized_H2Y8U4"/>
        <gene id="8795" protId="C6SUQ1" geneId="gpa2"/>
        <gene id="8797" protId="H2Z8J8" geneId="Csa.2035"/>
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        <gene id="8888" protId="H2YWV3" geneId="uncharacterized_H2YWV3"/>
        <gene id="8889" protId="H2Y8U9" geneId="uncharacterized_H2Y8U9"/>
        <gene id="8890" protId="H2YIJ6" geneId="uncharacterized_H2YIJ6"/>
        <gene id="8893" protId="H2ZNC6" geneId="uncharacterized_H2ZNC6"/>
        <gene id="8895" protId="H2YPW8" geneId="Csa.285"/>
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        <gene id="8915" protId="H2YSP2" geneId="uncharacterized_H2YSP2"/>
        <gene id="8916" protId="H2Z1U0" geneId="uncharacterized_H2Z1U0"/>
        <gene id="8917" protId="H2YFC2" geneId="uncharacterized_H2YFC2"/>
        <gene id="8918" protId="H2YBW1" geneId="uncharacterized_H2YBW1"/>
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        <gene id="8934" protId="H2Z997" geneId="Csa.10710"/>
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        <gene id="8970" protId="H2ZHP9" geneId="uncharacterized_H2ZHP9"/>
        <gene id="8971" protId="H2Y8X3" geneId="Csa.6104"/>
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        <gene id="8975" protId="H2YNJ9" geneId="uncharacterized_H2YNJ9"/>
        <gene id="8976" protId="H2Y496" geneId="uncharacterized_H2Y496"/>
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        <gene id="8978" protId="H2Y495" geneId="Csa.6635"/>
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        <gene id="8980" protId="H2YZN4" geneId="uncharacterized_H2YZN4"/>
        <gene id="8982" protId="H2ZPV2" geneId="uncharacterized_H2ZPV2"/>
        <gene id="8983" protId="H2ZPV1" geneId="Csa.10981"/>
        <gene id="8984" protId="H2YFM6" geneId="uncharacterized_H2YFM6"/>
        <gene id="8986" protId="H2YWX4" geneId="uncharacterized_H2YWX4"/>
        <gene id="8988" protId="H2YQJ6" geneId="uncharacterized_H2YQJ6"/>
        <gene id="8996" protId="H2YUG2" geneId="uncharacterized_H2YUG2"/>
        <gene id="8997" protId="H2YUI1" geneId="Csa.7299"/>
        <gene id="8998" protId="H2ZEV6" geneId="Csa.10065"/>
        <gene id="8999" protId="H2ZHQ0" geneId="uncharacterized_H2ZHQ0"/>
        <gene id="9000" protId="H2ZHQ2" geneId="uncharacterized_H2ZHQ2"/>
        <gene id="9001" protId="H2ZI22" geneId="uncharacterized_H2ZI22"/>
        <gene id="9005" protId="H2YSS0" geneId="Csa.3845"/>
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      </genes>
    </database>
    <notes>
      <additionalInformation abbreviation="C.savignyi" link="http://www.uniprot.org/taxonomy/51511"/>
    </notes>
  </species>
  <scores>
    <scoreDef id="bit" desc="BLAST score in bits of seed orthologs"/>
    <scoreDef id="inparalog" desc="Inparalog similarity relative to seed ortholog similarity"/>
    <scoreDef id="bootstrap" desc="Reliability of seed orthologs"/>
  </scores>
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      </geneRef>
      <geneRef id="2">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="2">
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="4">
        <score id="inparalog" value="0.244"/>
      </geneRef>
      <geneRef id="5">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="3">
      <score id="bit" value="2632"/>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="7">
        <score id="inparalog" value="0.761"/>
      </geneRef>
      <geneRef id="8">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="4">
      <score id="bit" value="2365"/>
      <geneRef id="9">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="10">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="5">
      <score id="bit" value="2097"/>
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        <score id="inparalog" value="1"/>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
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      <score id="bit" value="1866"/>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
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        <score id="bootstrap" value="1"/>
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        <score id="inparalog" value="0.961"/>
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        <score id="bootstrap" value="1"/>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
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        <score id="bootstrap" value="1"/>
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        <score id="inparalog" value="0.425"/>
      </geneRef>
      <geneRef id="24">
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        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
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        <score id="bootstrap" value="1"/>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="13">
      <score id="bit" value="1632"/>
      <geneRef id="35">
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        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="36">
        <score id="inparalog" value="0.338"/>
      </geneRef>
      <geneRef id="37">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
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