<?xml version="1.0" encoding="UTF-8" ?>
<!-- <!DOCTYPE scfg SYSTEM "../../lib/dtd/scfg.dtd" > -->
<!-- Control file for EvoFold v.1.0 (prev. v.13c) -->
<!-- This control file is based on the one used by RNA-decoder, which -->
<!-- was developed by Jakob Skou Pedersen and Irmtraud Meyer. -->
<!-- Jakob Skou Pedersen (jsp@soe.ucsc.edu) - December 4, 2005, Santa Cruz, Ca -->

<scfg-framework>
    <scfg_specification>
        <!--       THE ALIGNEMNT FILE POINTER:  -->
        <!--       The input alignment must be col format and a pointer defined as -->
        <!--       below. -->
        <observationSet id="input_alg" format="ama">
            <file name="input.ama" />
        </observationSet>
        <!--       THE PHYLOGENETIC TREE:  -->
        <!--       The tree must be in newick format, and use the names defined in -->
        <!--       the taxa list. -->
        <tree id="T_all">
            <newick>
                <file name="tree.newick" />
            </newick>
        </tree>
        <!--       THE SEQUENCE NAME LIST: -->
        <!--       The taxa list must correspond to the order of sequence -->
        <!--       input in the col file. It can be defined indirectly -->
        <!--       by the input alignment. -->
        <taxa id="TA_all">
            <observationSet idref="input_alg" />
        </taxa>
        <!--         Definition of alphabets: -->
        <fuzzyMetaNuc id="fuzzyMetaNuc" value="0.000" />
        <fuzzyMetaDiNuc id="fuzzyMetaDiNuc" value="0.000" />
        <!--    Definition of the evolutionary emission distributions:  -->
        <!--    Stem models :  -->
        <parameterizedConstrainedGTRDiNucModel id="SM_stem">
            <modelParameters>
                <compoundParameter id="stem.param">
                    <parameter id="stem.R_CG_AT" name="R_CG_AT" value="0.000342538" />
                    <parameter id="stem.R_GC_AT" name="R_GC_AT" value="213.344" />
                    <parameter id="stem.R_GC_CG" name="R_GC_CG" value="0.000271525" />
                    <parameter id="stem.R_GT_AT" name="R_GT_AT" value="3613.26" />
                    <parameter id="stem.R_GT_CG" name="R_GT_CG" value="0.00484582" />
                    <parameter id="stem.R_GT_GC" name="R_GT_GC" value="2644.86" />
                    <parameter id="stem.R_TA_AT" name="R_TA_AT" value="0.000750792" />
                    <parameter id="stem.R_TA_CG" name="R_TA_CG" value="145.611" />
                    <parameter id="stem.R_TA_GC" name="R_TA_GC" value="0.000121402" />
                    <parameter id="stem.R_TA_GT" name="R_TA_GT" value="0.00553353" />
                    <parameter id="stem.R_TG_AT" name="R_TG_AT" value="0.021412" />
                    <parameter id="stem.R_TG_CG" name="R_TG_CG" value="3332.72" />
                    <parameter id="stem.R_TG_GC" name="R_TG_GC" value="0.00146057" />
                    <parameter id="stem.R_TG_GT" name="R_TG_GT" value="0.162062" />
                    <parameter id="stem.R_TG_TA" name="R_TG_TA" value="3322.05" />
                    <parameter id="stem.R_NP_P" name="R_NP_P" value="7316.17" />
                    <parameter id="stem.R_NP_NP" name="R_NP_NP" value="0.358733" />
                </compoundParameter>
            </modelParameters>
            <frequencies>
                <compoundParameter id="stem.freq">
                    <parameter id="stem.AA" name="AA" value="0.00168548" />
                    <parameter id="stem.AC" name="AC" value="0.00399812" />
                    <parameter id="stem.AG" name="AG" value="0.0014503" />
                    <parameter id="stem.AT" name="AT" value="0.158631" />
                    <parameter id="stem.CA" name="CA" value="0.00407651" />
                    <parameter id="stem.CC" name="CC" value="0.00168548" />
                    <parameter id="stem.CG" name="CG" value="0.229853" />
                    <parameter id="stem.CT" name="CT" value="0.00207745" />
                    <parameter id="stem.GA" name="GA" value="0.00243023" />
                    <parameter id="stem.GC" name="GC" value="0.24608" />
                    <parameter id="stem.GG" name="GG" value="0.00211665" />
                    <parameter id="stem.GT" name="GT" value="0.0495061" />
                    <parameter id="stem.TA" name="TA" value="0.235379" />
                    <parameter id="stem.TC" name="TC" value="0.00219505" />
                    <parameter id="stem.TG" name="TG" value="0.0549545" />
                    <parameter id="stem.TT" name="TT" value="0.00388053" />
                </compoundParameter>
            </frequencies>
            <alphabetPointer idref="fuzzyMetaDiNuc" />
        </parameterizedConstrainedGTRDiNucModel>
        <!--    stem: -->
        <evoTree id="ET_stem">
            <tree idref="T_all" />
            <treeScale>
                <parameter id="TS_stem" name="scale" value="0.091327" />
            </treeScale>
            <substitutionModelPointer idref="SM_stem" />
            <taxa idref="TA_all" />
        </evoTree>
        <evoEmissionDistribution id="ED_stem" minPairDist="3" cardinality="2" useHashTable="true">
            <evoTreePointer idref="ET_stem" />
        </evoEmissionDistribution>
        <!--    non_pairing models:  -->
        <!--    non_pairing:  -->
        <marginalNucModel id="SM_non_pairing">
            <substitutionModelPointer idref="SM_stem" />
            <positions>
                <position value="0" />
                <position value="1" />
            </positions>
        </marginalNucModel>
        <evoTree id="ET_non_pairing">
            <tree idref="T_all" />
            <treeScale>
                <parameter id="SM_non_pairing.tree_scale" name="" value="0.218821" />
            </treeScale>
            <substitutionModelPointer idref="SM_non_pairing" />
            <taxa idref="TA_all" />
        </evoTree>
        <evoEmissionDistribution id="ED_non_pairing" cardinality="1" useHashTable="true">
            <evoTreePointer idref="ET_non_pairing" />
        </evoEmissionDistribution>
        <!--  grammar  -->
        <grammar>
            <!--  begin  -->
            <state id="begin" stateType="start" />
            <transition id="begin_to_NS" from="begin" to="NS">
                <parameter id="begin_to_NS.param" value="0.935115" />
            </transition>
            <transition id="begin_to_S" from="begin" to="S">
                <parameter id="begin_to_S.param" value="0.0648855" />
            </transition>
            <!--       intermediate_NS_S -->
            <state id="intermediate_NS_S" stateType="start" />
            <transition id="intermediate_NS_S-&gt;NS" from="intermediate_NS_S" to="NS">
                <parameter id="intermediate_NS_S-&gt;NS.param" value="0.929766" />
            </transition>
            <transition id="intermediate_NS_S-&gt;S" from="intermediate_NS_S" to="S">
                <parameter id="intermediate_NS_S-&gt;S.param" value="0.0702341" />
            </transition>
            <!--       NS -->
            <state id="NS" stateType="start" />
            <transition id="NS-&gt;bifurcation_NS" from="NS" to="bifurcation_NS">
                <parameter id="NS-&gt;bifurcation_NS.param" value="1" />
            </transition>
            <!--       bifurcation_NS -->
            <state id="bifurcation_NS" stateType="bifurcate" />
            <transition id="bifurcation_NS-&gt;begin_NS|S" from="bifurcation_NS" toLeft="begin_NS" toRight="S">
                <parameter id="bifurcation_NS-&gt;begin_NS|S.param" value="1" />
            </transition>
            <!--       S -->
            <state id="S" stateType="start" />
            <transition id="S-&gt;bifurcation_S" from="S" to="bifurcation_S">
                <parameter id="S-&gt;bifurcation_S.param" value="0.532977" />
            </transition>
            <transition id="S-&gt;end" from="S" to="end">
                <parameter id="S-&gt;end.param" value="0.467023" />
            </transition>
            <!--       bifurcation_S -->
            <state id="bifurcation_S" stateType="bifurcate" />
            <transition id="bifurcation_S-&gt;begin_S|intermediate_NS_S" from="bifurcation_S" toLeft="begin_S" toRight="intermediate_NS_S">
                <parameter id="bifurcation_S-&gt;begin_S|intermediate_NS_S.param" value="1" />
            </transition>
            <!--        begin_NS -->
            <state id="begin_NS" stateType="start" />
            <transition id="begin_NS-&gt;left_NS" from="begin_NS" to="left_NS">
                <parameter id="begin_NS-&gt;left_NS.param" value="1" />
            </transition>
            <!--       left_NS -->
            <state id="left_NS" stateType="left" emissionDistribution="ED_non_pairing">
                <labelSet>
                    <labelType typeName="pairingmask" leftLabel="." />
                    <labelType typeName="stateAnno" leftLabel="NS" />
                </labelSet>
            </state>
            <transition id="left_NS-&gt;left_NS" from="left_NS" to="left_NS">
                <parameter id="left_NS-&gt;left_NS.param" value="0.958403" />
            </transition>
            <transition id="left_NS-&gt;end" from="left_NS" to="end">
                <parameter id="left_NS-&gt;end.param" value="0.0415971" />
            </transition>
            <!--        begin_S -->
            <state id="begin_S" stateType="start" />
            <transition id="begin_S-&gt;pair" from="begin_S" to="pair">
                <parameter id="begin_S-&gt;pair.param" value="1" />
            </transition>
            <!--       intermediate -->
            <state id="intermediate" stateType="start" />
            <transition id="intermediate_to_bifurcation" from="intermediate" to="bifurcation">
                <parameter id="intermediate_to_bifurcation.param" value="0.590478" />
            </transition>
            <transition id="intermediate_to_emit" from="intermediate" to="emit">
                <parameter id="intermediate_to_emit.param" value="0.409522" />
            </transition>
            <!--       bifurcation -->
            <state id="bifurcation" stateType="bifurcate" />
            <transition id="bifurcation-&gt;emit|intermediate" from="bifurcation" toLeft="emit" toRight="intermediate">
                <parameter id="bifurcation-&gt;emit|intermediate.param" value="1" />
            </transition>
            <!--       emit -->
            <state id="emit" stateType="start" />
            <transition id="emit-&gt;left_S" from="emit" to="left_S">
                <parameter id="emit-&gt;left_S.param" value="0.821553" />
            </transition>
            <transition id="emit-&gt;pair" from="emit" to="pair">
                <parameter id="emit-&gt;pair.param" value="0.178447" />
            </transition>
            <!--       left_S -->
            <state id="left_S" stateType="left" emissionDistribution="ED_non_pairing">
                <labelSet>
                    <labelType typeName="pairingmask" leftLabel="." />
                    <labelType typeName="stateAnno" leftLabel="S" />
                </labelSet>
            </state>
            <transition id="left_S-&gt;left_S" from="left_S" to="left_S">
                <parameter id="left_S-&gt;left_S.param" value="0.686756" />
            </transition>
            <transition id="left_S-&gt;end" from="left_S" to="end">
                <parameter id="left_S-&gt;end.param" value="0.313244" />
            </transition>
            <!--       end   -->
            <state id="end" stateType="end" />
            <!--       pair -->
            <state id="pair" stateType="pair" emissionDistribution="ED_stem">
                <labelSet>
                    <labelType typeName="pairingmask" leftLabel="(" rightLabel=")" />
                    <labelType typeName="stateAnno" leftLabel="(" rightLabel=")" />
                </labelSet>
            </state>
            <transition id="pair-&gt;pair" from="pair" to="pair">
                <parameter id="pair-&gt;pair.param" value="0.797853" />
            </transition>
            <transition id="pair-&gt;bifurcation" from="pair" to="bifurcation">
                <parameter id="pair-&gt;bifurcation.param" value="0.202147" />
            </transition>
            <!--       High level structures - automatically composed from the -->
            <!--       above defined objects. -->
            <transitionSet id="fold.transitionSet" />
            <stateSet id="fold.stateSet" />
        </grammar>
        <scfg id="fold" name="fold" version="v.13" author="Jakob S. Pedersen" created="15 Nov 04" description="an SCFG for RNA sec struct.">
            <transitionSet idref="fold.transitionSet" />
            <stateSet idref="fold.stateSet" />
            <emissionDistributionSet id="fold.emissionDistributionSet">
                <stateSet idref="fold.stateSet" />
            </emissionDistributionSet>
        </scfg>
        <grammar>
            <!--  begin  -->
            <state id="nonStr_begin" stateType="start" />
            <transition id="nonStr_begin_to_left_NS" from="nonStr_begin" to="nonStr_left_NS">
                <parameter id="nonStr_nonStr_begin_to_nonStr_left_NS.param" value="1" />
            </transition>
            <!--       left_NS -->
            <state id="nonStr_left_NS" stateType="left" emissionDistribution="ED_non_pairing">
                <labelSet>
                    <labelType typeName="pairingmask" leftLabel="." />
                    <labelType typeName="stateAnno" leftLabel="NS" />
                </labelSet>
            </state>
            <transition id="nonStr_left_NS-&gt;nonStr_left_NS" from="nonStr_left_NS" to="nonStr_left_NS">
                <parameter id="nonStr_left_NS-&gt;nonStr_left_NS.param" value="0.989896" />
            </transition>
            <transition id="nonStr_left_NS-&gt;nonStr_end" from="nonStr_left_NS" to="nonStr_end">
                <parameter id="nonStr_left_NS-&gt;nonStr_end.param" value="0.0101037" />
            </transition>
            <!--       end   -->
            <state id="nonStr_end" stateType="end" />
            <!--       High level structures - automatically composed from the -->
            <!--       above defined objects. -->
            <transitionSet id="nonStr.transitionSet" />
            <stateSet id="nonStr.stateSet" />
        </grammar>
        <scfg id="nonStr" name="NS" version="v.13" author="Jakob S. Pedersen" created="15 Nov 04" description="an SCFG for RNA sec struct.">
            <transitionSet idref="nonStr.transitionSet" />
            <stateSet idref="nonStr.stateSet" />
            <emissionDistributionSet id="nonStr.emissionDistributionSet">
                <stateSet idref="nonStr.stateSet" />
            </emissionDistributionSet>
        </scfg>
        <!-- scfg body ends here -->
    </scfg_specification>
    <!--       Specifies a model, a data set and the type of analysis to perform -->
    <analysis>
        <scfg idref="fold" />
        <observationSet idref="input_alg" />

      <reportFile>
	<file name="S_report.txt" />
      </reportFile>
      <inside>
	<verbose level="1" />
      </inside>

      <!--     <writeGrammarInfo> -->
      <!--       <verbose level="1" /> -->
      <!--     </writeGrammarInfo> -->
      <!--         <writeDotGraph> -->
      <!--           <verbose level="1" /> -->
      <!--           <file name="./output/ranking_v.13.dot" /> -->
      <!--         </writeDotGraph> -->

      <!--         <optimize emissions="" transitions="" deltaDiff="0.001" maxIter="2"> -->
      <!--             <verbose level="1" /> -->
      <!--         </optimize> -->
      <!--         <write> -->
      <!--             <verbose level="1" /> -->
      <!--             <file name="./ranking_v.13_est.xml" /> -->
      <!--         </write> -->

      <cyk calculatePostProbs = "true" annotatePairedPos = "true" >
	<verbose level="1" />
	<file name="cyk.ama" format="ama" />
      </cyk>

      <!--         <posteriourDecoding restricted = "true" calculatePostProbs = "true" annotatePairedPos = "true" > -->
      <!--           <verbose level="1" /> -->
      <!--           <file name="./output/test_pd.ama" format="ama"/> -->
      <!--         </posteriourDecoding> -->
      <!--     <resetAnnotationUse> -->
      <!--       <verbose level="1" /> -->
      <!--       <labelSet> -->
      <!--     	<labelType typeName="pairingmask"   /> -->
      <!--       </labelSet> -->
      <!--     </resetAnnotationUse> -->
      <!--     <statePosteriorProb> -->
      <!--       <verbose level="1" /> -->
      <!--       <stateList> -->
      <!-- 	    	 	  List of state representatives for the labels which posterior -->
      <!-- 	    	 	  probabilities should be calculated for. 'left'_S is the loop -->
      <!-- 	    	 	  state and 'left_NS' is a representative for the -->
      <!-- 	    	 	  non-structural states. -->
      <!-- 	<state idref="left_S" /> -->
      <!-- 	<state idref="left_NS" /> -->
      <!--       </stateList> -->
      <!--       <file name="scanning.ama" format="ama" /> -->
      <!--     </statePosteriorProb> -->
    </analysis>
  <!--       Specifies a model, a data set and the type of analysis to perform -->
  <analysis>
    <scfg idref="nonStr" />
    <observationSet idref="input_alg" />

    <reportFile>
      <file name="NS_report.txt" />
    </reportFile>
    <inside>
      <verbose level="1" />
    </inside>

    <!--     <writeGrammarInfo> -->
    <!--       <verbose level="1" /> -->
    <!--     </writeGrammarInfo> -->
    <!--         <writeDotGraph> -->
    <!--           <verbose level="1" /> -->
    <!--           <file name="./output/ranking_v.13.dot" /> -->
    <!--         </writeDotGraph> -->
    <!--         <resetAnnotationUse> -->
    <!--             <verbose level="1" /> -->
    <!--             <labelSet /> -->
    <!--         </resetAnnotationUse> -->
    <!--         <optimize transitions="" deltaDiff="0.001" maxIter="1"> -->
    <!--             <verbose level="1" /> -->
    <!--         </optimize> -->
    <!--         <write> -->
    <!--             <verbose level="1" /> -->
    <!--             <file name="./ranking_v.13_est.xml" /> -->
    <!--         </write> -->
    <!--       <cyk calculatePostProbs = "true" annotatePairedPos = "true" > -->
    <!-- 	<verbose level="1" /> -->
    <!-- 	<file name="cyk.ama" format="ama" /> -->
    <!--       </cyk> -->
    <!--         <posteriourDecoding restricted = "true" calculatePostProbs = "true" annotatePairedPos = "true" > -->
    <!--           <verbose level="1" /> -->
    <!--           <file name="./output/test_pd.ama" format="ama"/> -->
    <!--         </posteriourDecoding> -->
    <!--     <statePosteriorProb> -->
    <!--       <verbose level="1" /> -->
    <!--       <stateList> -->
    <!-- 	    	 	  List of state representatives for the labels which posterior -->
    <!-- 	    	 	  probabilities should be calculated for. 'left'_S is the loop -->
    <!-- 	    	 	  state and 'left_NS' is a representative for the -->
    <!-- 	    	 	  non-structural states. -->
    <!-- 	<state idref="left_S" /> -->
    <!-- 	<state idref="left_NS" /> -->
    <!--       </stateList> -->
    <!--       <file name="scanning.ama" format="ama" /> -->
    <!--     </statePosteriorProb> -->
  </analysis>
</scfg-framework>
