#NEXUS

BEGIN TAXA;
      dimensions ntax=8;
      taxlabels A B C D E F G H;  
END;

BEGIN CHARACTERS;
      dimensions nchar=6;
      format datatype=protein missing=? gap=-;
      charlabels one two three four five six;
      matrix
A     WITH--
B     WITH--
C     WITH--
D     WITH--
E     WITH--
F     WITH--
G     WITH--
H     WITH--;
END;

BEGIN TREES;
	[this file tests the equlity of the tree _topology_ a separate test should performed to compare node attributes (such as NHX comments, bootstrap values, etc)]

	tree bush =	(((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1);
	tree bush_isomer = (((A:1,B:1):1,(C:1,D:1):1):1,((G:1,H:1):1,(E:1,F:1):1):1);
	tree bush_diff = (((D:1,B:1):1,(C:1,A:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1);
	
	tree ladder_one = (((A:1,B:1):1,C:1):1,D:1);
	tree ladder_one_isomer_1 = (((B:1,A:1):1,C:1):1,D:1);
	tree ladder_one_isomer_2 = ((C:1,(A:1,B:1):1):1,D:1);
	tree ladder_one_diff = (((A:1,B:1):1,D:1):1,C:1);
	
	tree rake_one = (A:1,B:1,C:1,D:1,E:1,F:1,G:1,H:1);
	tree rake_one_isomer_1 = (A:1,B:1,D:1,C:1,E:1,F:1,H:1,G:1);
	tree rake_one_diff = (A:1,B:1,C:1,D:1,E:1,F:1,G:1);
	
	tree thing_one = (((A,B),C),(D,E));
	tree thing_one_isomer_1 = ((C,(A,B)),(D,E));
	tree thing_one_diff = (((D,E),C),(A,B));
	
	tree thing_two = (A,(B,C),(D,E));
	tree thing_two_isomer_1 = (A,(D,E),(B,C));
	tree thing_two_diff = (A,B,C,D,E);
	
	tree TF342628 = (A:0.00161[&&NHX:G=ENSG00000189395:O=ENST00000342416.2:S=HUMAN],((B:0[&&NHX:G=ENSG00000205275:O=ENST00000338938.2:S=HUMAN],C:0[&&NHX:G=ENSG00000188384:O=ENST00000342039.2:S=HUMAN])inode3:0[&&NHX:B=10:D=Y:S=HUMAN],D:0[&&NHX:G=ENSG00000205271:O=ENST00000379430.1:S=HUMAN])inode2:0.00161[&&NHX:B=10:D=Y:S=HUMAN])root[&&NHX:B=0:D=Y:S=HUMAN];
	tree TF342628_diff_1 = (A:1[&&NHX:G=ENSG00000189395:O=ENST00000342416.2:S=HUMAN],((B:0[&&NHX:G=ENSG00000205275:O=ENST00000338938.2:S=HUMAN],C:0[&&NHX:G=ENSG00000188384:O=ENST00000342039.2:S=HUMAN])inode3:0[&&NHX:B=10:D=Y:S=HUMAN],D:0[&&NHX:G=ENSG00000205271:O=ENST00000379430.1:S=HUMAN])inode2:0.00161[&&NHX:B=10:D=Y:S=HUMAN])root[&&NHX:B=0:D=Y:S=HUMAN];

	tree nhx_one = (((A:1[&&NHX:S=human:E=1],B:1[&&NHX:S=human:E=1]):1,C:1[&&NHX:S=Primates:E=1:D=Y:B=100]):1,D:1[&&NHX:S=nematode:E=1]);
	[changing a tag in 'A']
	tree nhx_one_diff_1 = (((A:1[&&NHX:S=chimp:E=1],B:1[&&NHX:S=human:E=1]):1,C:1[&&NHX:S=Primates:E=1:D=Y:B=100]):1,D:1[&&NHX:S=nematode:E=1]);
	[removing an nhx comment completely]
	tree nhx_one_diff_2 = (((A:1,B:1[&&NHX:S=human:E=1]):1,C:1[&&NHX:S=Primates:E=1:D=Y:B=100]):1,D:1[&&NHX:S=nematode:E=1]);
	
	tree attr_one = ((A:1,B:1),(C:1,D:1),(E:1,F:1));
	tree attr_one_diff_1 = ((A:2,B:1),(C:1,D:1),(E:1,F:1));
	tree attr_one_diff_2 = ((A:1,B:1):1,(C:1,D:1),(E:1,F:1));
	tree attr_one_diff_3 = ((A:1,B:1),(C:1,D:1),(E:1,F:1)):1;
	
	[need challenging examples...]
	[need trees with NHX comments...]
	
END;