#NEXUS
[! Output from Cipres Rec-I-dcm3 with the following settings:
      Max Iterations = 2
      Max RunHours = 0
      Max SubsetSize = 20
      Max RecursionLevel = 0
      Large Tree Improver = alex-borchers-powerbook-g4-15.local,IDL:CipresIDL/TreeImprove:1.0,org.cipres.paup-wrap,Python wrapper around PAUP's HSearch command (using parsimony). file-based io.
              Parameters  =  set Increase=Auto; set AutoInc=100; Default HS swap=tbr multrees=no  timelimit=None reconlimit=Infinity;
      Small Tree Improver  = alex-borchers-powerbook-g4-15.local,IDL:CipresIDL/TreeImprove:1.0,org.cipres.paup-wrap,Python wrapper around PAUP's HSearch command (using parsimony). file-based io.
              Parameters  =  set Increase=Auto; set AutoInc=100; Default HS swap=tbr multrees=no  timelimit=None reconlimit=Infinity;
      Tree Decomposer  = alex-borchers-powerbook-g4-15.local,IDL:CipresIDL/TreeDecompose:1.0,org.cipres.dcm3,Roshan DCM
      Tree Merger  = alex-borchers-powerbook-g4-15.local,IDL:CipresIDL/TreeMerge:1.0,org.cipres.PhycasSCMTreeMerge,C++ implementation of SCM (Yu Fan and Paul Lewis)
      Tree Refiner  = alex-borchers-powerbook-g4-15.local,IDL:CipresIDL/TreeRefine:1.0,org.cipres.random-refine,Python implementation of a random refinement of polytomies (Random seed hard-coded for debugging purposes)
 Using the datamatrix and starting tree from /Users/borchers/CIPRES_dev/CIPRES-1.0.1/cipres/cipres_dist/help/sampleFiles/TestNexusFile.nex
 Final tree is = Iteration 2 (0h:0m:6s) and has score = 331
]
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;
  Tree 'Starting Tree' [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);
  Tree 'Iteration 1 (0h:0m:5s)'[Score=331] = [&U](1:22.0,2:26.0,(((3:17.0,(4:3.0,5:9.0):20.0):4.0,(11:22.0,12:18.0):38.0):10.0,((((6:0,7:13.0):15.0,8:6.0):19.0,9:29.0):16.0,10:22.0):11.0):11.0);
  Tree 'Iteration 2 (0h:0m:6s)'[Score=331] = [&U](1:22.0,2:26.0,(((3:17.0,(4:3.0,5:9.0):20.0):4.0,(11:22.0,12:18.0):38.0):10.0,((((6:0,7:13.0):15.0,8:6.0):19.0,9:29.0):16.0,10:22.0):11.0):11.0);
END;