#NEXUS

[! Output from rid3-raxml using the data matrix from data.nex
and starting tree from data.nex

The following settings were used for the analysis:

org.cipres.recidcm3 Parameters:
    SetTreeDecompModule=*,IDL:CipresIDL_api1/TreeDecompose:1.0,org.cipres.dcm3,Roshan DCM
    SetLargeTreeInferenceModule=*,IDL:CipresIDL_api1/TreeImprove:1.0,org.cipres.raxml,Python wrapper around RAxMLHPC. file-based io.
    SetSmallTreeInferenceModule=*,IDL:CipresIDL_api1/TreeImprove:1.0,org.cipres.raxml,Python wrapper around RAxMLHPC. file-based io.
    SetTreeRefineModule=*,IDL:CipresIDL_api1/TreeRefine:1.0,org.cipres.random-refine,Python implementation of a random refinement of polytomies (Random seed hard-coded for debugging purposes)
    SetTreeMergeModule=*,IDL:CipresIDL_api1/TreeMerge:1.0,org.cipres.PhycasSCMTreeMerge,C++ implementation of SCM (Yu Fan and Paul Lewis)
    SetMaxTaxaSubsetPercent=50;
    SetMaxIterations=10;
    ignoreStartEdgeLen=no;

Tree Decomposer Module Parameters:
    BreakTies=yes;
    SEED=0;

Large Tree Inference Module Parameters:
    -c 25
    -m GTRGAMMA
    -i 10

Large Tree Inference Module Parameters:
    -c 25
    -m GTRGAMMA
    -i 10

]

BEGIN TAXA;
      Dimensions ntax=12;
      Taxlabels a b c d e f g u v x y t ;
END;

BEGIN TREES;
   Translate
      1   a,
      2   b,
      3   c,
      4   d,
      5   e,
      6   f,
      7   g,
      8   u,
      9   v,
      10   x,
      11   y,
      12   t;

[Starting Tree(s)]
  Tree rep.1[Score=UNSCORED] = [&U]((((1:.1,2:1):1,(12:3.2,7:1):2):1,(3:2,4:1):1):1,(((5:1,6:1):1,8:1):1,9:1.2,(10:0.2,11:1):1):1);

[Result Tree(s)]
  Tree 'Iteration 1 (0h:0m:12s) unnamed_tree_0'[Score=-2157.458839] = [&U](((((11:0.0402134409003,12:0.0703791636747):0.146923115324,3:0.0443434337078):0.00703923641841,2:0.0859973913637):0.00921432465123,(4:0.00862368879072,5:0.0210714051243):0.0601395965455):0.0145309296235,(10:0.0769906500612,(9:0.116025680718,(8:0.03007950279,(6:1.36301333676e-06,7:0.0326414990336):0.0244695578388):0.0480649268473):0.0169463209065):0.0275762098573,1:0.0636886096066):0;
  Tree 'Iteration 2 (0h:0m:19s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0;
  Tree 'Iteration 3 (0h:0m:25s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0;
  Tree 'Iteration 4 (0h:0m:31s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0;
  Tree 'Iteration 5 (0h:0m:38s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0;
  Tree 'Iteration 6 (0h:0m:44s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0;
  Tree 'Iteration 7 (0h:0m:52s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0;
  Tree 'Iteration 8 (0h:1m:1s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0;
  Tree 'Iteration 9 (0h:1m:9s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0;
  Tree 'Iteration 10 (0h:1m:15s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0;
END;