APPENDIX 2

An example NEXUS file with StrataPhy block.

#NEXUS
BEGIN TAXA;
     DIMENSIONS  NTAX=6;
     TAXLABELS Taxon_1 Taxon_2 Taxon_3 Taxon_4 Taxon_5 Taxon_6;
END;
BEGIN CHARACTERS;
     DIMENSIONS  NCHAR=7;
     FORMAT SYMBOLS= " 0 1 2 3 4 5" MISSING=? GAP=- ;
MATRIX
Taxon_1   0000000
Taxon_2   1000001
Taxon_3   1100002
Taxon_4   1110003
Taxon_5   1112004
Taxon_6   1112105
;
END;
BEGIN ASSUMPTIONS;
     TYPESET * UNTITLED = ord: 1-6, strat: 7;
     TYPESET unord_only = unord: 1-6, strat: 7;
     WTSET * UNTITLED = 1.00: 1-7;
     WTSET variable = 2.00: 1-3, 1.00: 4-7;
     EXSET UNTITLED = 4-6;
     EXSET * stored_1 = 4;
END;
BEGIN TREES;
     TRANSLATE
          1    Taxon_1,
          2    Taxon_2,
          3    Taxon_3,
          4    Taxon_4,
          5    Taxon_5,
          6    Taxon_6
     ;
     TREE  * Tree1 =  [&R] (((((6)5)4)3)2)1;
END;
BEGIN STRATAPHY;
          MAXTREES = 1000;
          SEARCHREPS = 10;
          ANCREPS = 1;
          ANCTYPE = heuristic;
          outgroup Taxon_1 Taxon_2;
END;