<?xml version="1.0" encoding="utf-8"?>
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  <notes>
    <stats ortholog_groups="343" inparalogs="901"/>
    <parameters scoreCutoff="40" confidenceCutoff="0.05" overlapCutoff="0.5" mergingCutoff="0.5" matrix="BLOSUM62"/>
  </notes>
  <species name="Halobacterium salinarum " NCBITaxId="64091">
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    <notes>
      <additionalInformation abbreviation="H.salinarum" link="http://www.uniprot.org/taxonomy/64091"/>
    </notes>
  </species>
  <species name="Scheffersomyces stipitis " NCBITaxId="322104">
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        <gene id="452" protId="A3GGY9" geneId="PICST_80857"/>
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        <gene id="582" protId="A3GF08" geneId="VMA8"/>
        <gene id="584" protId="A3LQB2" geneId="NTG2"/>
        <gene id="586" protId="A3LX67" geneId="RPS1B"/>
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        <gene id="589" protId="A3GHI8" geneId="PICST_86681"/>
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        <gene id="597" protId="A3GEZ4" geneId="GUT2"/>
        <gene id="599" protId="A3LPJ5" geneId="OGG1"/>
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        <gene id="606" protId="A3LQ01" geneId="DED1"/>
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        <gene id="611" protId="A3GGL0" geneId="PICST_28646"/>
        <gene id="613" protId="A3GI76" geneId="PICST_39982"/>
        <gene id="615" protId="A3LTA4" geneId="PICST_89215"/>
        <gene id="618" protId="A3LSV4" geneId="HIS5"/>
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        <gene id="665" protId="A3GH28" geneId="MDHM"/>
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        <gene id="833" protId="A3GI07" geneId="PICST_53707"/>
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        <gene id="850" protId="A3LR26" geneId="PICST_77026"/>
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        <gene id="864" protId="A3LWA3" geneId="PICST_59713"/>
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        <gene id="871" protId="A3LSG4" geneId="RPS29A"/>
        <gene id="873" protId="A3LTZ7" geneId="ASN1"/>
        <gene id="876" protId="A3LRY6" geneId="PICST_44059"/>
        <gene id="878" protId="A3GFY9" geneId="RPC25"/>
        <gene id="880" protId="A3LQI9" geneId="RPL39B"/>
        <gene id="882" protId="A3LQ79" geneId="PPA2"/>
        <gene id="883" protId="A3LTU4" geneId="IPP1"/>
        <gene id="885" protId="A3GFV7" geneId="RIB4"/>
        <gene id="887" protId="A3LWP2" geneId="PICST_62767"/>
        <gene id="889" protId="A3GFX8" geneId="RPS27"/>
        <gene id="890" protId="A3LZ02" geneId="RS27B"/>
        <gene id="892" protId="A3LUD7" geneId="PICST_59509"/>
        <gene id="894" protId="A3LYZ0" geneId="PICST_63621"/>
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        <gene id="901" protId="A3GGS4" geneId="PICST_69049"/>
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    </database>
    <notes>
      <additionalInformation abbreviation="S.stipitis" link="http://www.uniprot.org/taxonomy/322104"/>
    </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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        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="2">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="2">
      <score id="bit" value="606"/>
      <geneRef id="3">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="0.99"/>
      </geneRef>
      <geneRef id="4">
        <score id="inparalog" value="0.437"/>
      </geneRef>
      <geneRef id="5">
        <score id="inparalog" value="0.179"/>
      </geneRef>
      <geneRef id="6">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="0.99"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="3">
      <score id="bit" value="603"/>
      <geneRef id="7">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="8">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="0.97"/>
      </geneRef>
      <geneRef id="9">
        <score id="inparalog" value="0.11"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="4">
      <score id="bit" value="567"/>
      <geneRef id="10">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="11">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="0.99"/>
      </geneRef>
      <geneRef id="12">
        <score id="inparalog" value="0.088"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="5">
      <score id="bit" value="534"/>
      <geneRef id="13">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="14">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="6">
      <score id="bit" value="514"/>
      <geneRef id="15">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="16">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="7">
      <score id="bit" value="512"/>
      <geneRef id="17">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="18">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="19">
        <score id="inparalog" value="0.093"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="8">
      <score id="bit" value="486"/>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="0.98"/>
      </geneRef>
      <geneRef id="21">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="22">
        <score id="inparalog" value="0.409"/>
      </geneRef>
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</orthoXML>
