#NEXUS 

[This file contains two simulated DNA data sets, an assumption block, a sets block, 
 and a paup block.  Commands used in the sets block define the characters 
 representing each simulated data set.  Commands used in the assumption block define
 a usertype that weights transversions 10 times transitions. Both data sets were 
 simulated on the same tree; however, the first data set (d1) has a transition bias
 that when uncorrected causes a parsimony analysis to find the wrong tree.   
 The following numbered list corresponds with the numbered lines in the PAUP block.
 (1)  Automatically close the status window when an action completes. 
 (2)  Conduct a partition homogeneity test (ILD test of Farris, 1995) using the "genes"
      character partition. The seed value for the random number generator is set to 
	  one. 
 (3)  Include only the d1 data set.
 (4)  Conduct a heuristic search using default settings and show the tree.
 (5)  Include only the d2 data set.
 (6)  Conduct a heuristic search using default settings and show the tree.
 (7)  Include all the data.
 (8)  Weight tranversions 10 times transitions for the d1 data set only.
 (9)  Conduct a partition homogeneity test (ILD test of Farris, 1995) using the "genes"
      character partition and the 10_1 transversion weighting for the d1 data set.
	  The seed value for the random number generator is set to one.
 (10) Repeat steps 3-6 with tranversions weighted 10 times transitions.
]
Begin taxa;
  Dimensions ntax=8;
  taxlabels
A
B
C
D
E
F
G
H
;
End;

Begin data;
	Dimensions ntax=8 nchar=1200;
	Format datatype=dna interleave;
	Matrix
        [Start of d1]
		A ATAAGTCCAAGCGATAACTACACACGCCCAGCGGCAACCAAGAGGCAACAACAACACGAACAAGGAGGAAACAAAGAACAACAAGCGGCAACAAACAAAAGGGAAAAGCCCGACCGCGAAGCAGAACGAACCCAACCACACACAACACCGAAAAAAGCCGAGACGAAGAGAAAGGAAACCAAAAACACGCCCACCCGAATAGAAGATAACCCAGCCACTACTAACACGAACGCCCAACCCAGAGAAGCAAGAGACGCAGTCGCAGGAACGCTCGCCCCAGCAAAAGTACAACAACGAAAACCCGAGGACGAGACGCCAAGAAGGGGGAGTGCGAACTCAAGTAAAGAAAAACGATGAGCATTCATCAAACTACTGCAGAACAGGGCAAGACCAGCAAAATAAAAGAACCAAATAAAGCGAACAGGGCGACCCTAAAGCAACAGATATCAGCGCACGAAATTGAACAGCACACGAAAAAAAACACACGCGACTAATCAAAAACAAGAGGGCACGCCGCGAAGAGCGACCAGTGAGGAACCCAAGAACAACACCGAGACCACGAAACAGAACCTCTCCGAACGAAGCCGGACACGAAAGCAT
		B GCAGATAGGAACGGCGGAACTAAGCAACAGCCAGCACACAACGACAGAAAGCAGCATACGAGAAGGGCAAGCGAGAGATAACCAAACACAACGAGACAGAAGGGAAAGCCCGAACGCGGCGGAAGGTAAAGTCGATCGCCCGCGAGACAGGCACAAAGTCAGACAAGAGAAAGGAAATCCGGAGCCAAACCGACCTAGCAAAAAAACCGAACAAGCATCGACGGTATGAAAACACAACACGACAACACAACGATGACGACCAAAAGGATAACTGCCCTAACGAAAAGAAAAACCAAAGGGCCCAGAAGACGAGAGGCAGAGAAGAAGAAGGAAGACCCGGGCGGAAGAACAAGACAAGCGCTGATGCAGCCATGAAGAAAAGGAAACAAAAAAGGGGGAGACACAGCCCAGACACGGCAGGCATCAGGGCCCGAGGAGGGCCGGAAACAAAACACAGGACCCGACCGCCGCCAAAAAACAAGAAAGAAACCAGGCTGGAAACGAAGAAGGAGACAGAAAGAAACTATTCACAAAAGACCTAGGAGCCAAACTGAGAGCGAGAAATATAATCACCCGGAGAGAGACCAAGTGCAACTCCAT
		C GCAAATAAGCATACCGGCCATGCAGGCCCAGCAACGGTCAACGGATGACGGTTGCGGGAGCGAAAGAGGTAAAAAAAACGACCGGCAATGAAGAGGCAAAAGGGAAGGGCCGGCGACAACAGAAATCGAAGCCGGCAACACAACGAACCGGTGTGCAGGAAGTCGCAGAGAACGAGAAACAAAAGCGCACCAGCTAAATAAAGAAGTAAGATGACAAACATGAAGACGGACACGAGACGAGGAGAAACGGCAGTCACGATAAAGAAGATGACGACCGCGCAAAAAAGAGGGAAACAGAACCTCAGGAGCGACGCACCAAAGACAAGAAGTAAGACCCCAAGCAGAAGCGGGAGACAAACACTCCTAAGCCAACCAAAAAAAAAAACCGAAACAAAGAAAAACCCAGGCCAAGAAGAGAAAACATCCAAGATCAAGGACGGTGAGCGCCAGGACACCGAACGAGACCACAATCAAAAAGGAATAGAAACAAAGAACTGAATACAAAAAGAGACCCGGAGGACGAACTCCCACGGAGGGTCCGAAGACCATAGCAAAGCCAACAAACGACCACGCACAAACCCAGGTAAGATACAGAGGCAC
		D GAGCACAAAGACGGCGGCGAAGCGTACCAAACAGCAGTCGGAAAACAGCAGCTACGCATACGAAAAGGAAACAAAGGACAACCAGAAATAGAACGCCAGGGGGAAAAACCCGGCCACACTAAGAACCAAGACCGGCCACGCGCAAAAACAGGGCACAAAAAAACACAAAAAAGGAGACACACGACCAAACCAGACAGATGAGAAAGCGAGACGGCCACAACCGGAGTAGATAAAGAACGCTAAGAAGTGACCACCGCAGTAAAAGTAGTAGCAATCTCGCCAAAAGGAAGAAGCCGGACGGTCAAGAGAAAGGAGGTAGGAGCGAGCGACAAGAACCCGGACAACGGAAGAGGGCAAGGACCCCCTAACGAGGCGAAAACGGGAACAAAAACAAGAGAGAACACAAACCGAACAGGAAACGCATCCAAACCAGAAGACAACAAACATAAGAGCACAAAATCAGAGACCAACCGAACAGAGACAAGAACGCAAAATTAGGGGGAGAGGAAAGCGCGAAGCAGAACAACCCGCGAAAAACATGGAAAACGCACTAAAAACGGCAGATAAACCCACACGAGACCAGAACGAATGTAAGAACAC
		E GCACACGAAAGCAACAATGATCTACGACAAGCAGGGGTCATAAAAGAAGGACCGCAGAGACAGAACAGGAACGGAGGGCAACAAGCAACGAGCAACCCGAAGAAGGAACCCGCCCACAGCACAAGGCAGACTTGATCACACACGGAGCCAGCAGAAGGGGGAACCGAAGGCGCAAAATACAACATAAAACCACCCAAACAGAGGGACAAGAAGACTGCTGCCAACATAGCCGCAAATCACGGGGAAACAGCCGCCGCGACAGAGGGAAAAAGAAAACCCACACGCGAAAGGAGCGAAATGCCCAAAAAGGGGAGACGAGAAAGCGAAAAACGCGATGCAAGACGGAGCAAAAAATGGACAACCCTAAGCCCACCAAACACGAAAGCGAGGGCCAATAAAACCCCAAACCCCACGGAGGAAGCTCGCAGACCAAGAAGAAATAAACAACCGAAAGCGCAGACAAACGGTAAACAAAGAAGAGTGACGATCTGACATCAAAAGAAGGAGAAAGCAAACAAGGCAACCGCCAATAGGGAATCGGCAAAGTCTAACGAGCGCAACGCTCGCCCCCACACCCAACCAAACCAGACCGAGAAATAC
		F CCCCACAAAAAAGACAATAATCTGCGACAAGCACAAGTCATAAAAGAAGGACCGCGCAAACAAAAACAGAACAGAGAGCGACAAATGATGACCAACCCGAAGAAGGAACCCGCCCACGACACAAGGCAGACTTGATCGCACACAAGGCCAACAGAAGGAGAAGCCAAAAATGCAAGATACACCGCAAAACCGCCCAAACAGAGGAACAAGAACACAACGGCCGCCACAGGCACGAACCGCAGAGAAACAACCACCACGAGAGAAAAAAAAAGAAAACCCACACAGGAAAGAACCAGAATGCCCGAAAGGAGAAGGCAAAGTAACGAGAAGCAGGGCGCAAGACAGAGCAAGGGAGGGACGACCCCAGACCCACCAAACACCAAAGCGGGGGCTAACGAAGGCCAAAATCCCACAAAGAAAACTTGCAAACCGAGGAGAAGCGGACATCCGAAAGCACAAGCAAACGGCGGGCAAAAAAGCATAACGGCATAAGACCAAGAGAGAAGGACAACAGGCAGAGCAACCACCAGTGAGGAATCAGCGAGGTCTAACGAACGCTACGCACACCACCACGTTCAATCGAACCAGGCCGAGAAATGT
		G GGCAACGCAGCGGCCAACAATGCGCAGCAGGAGGAAAATAGGAAAGGCAGTACGCGTGAGAAGGCACGCAATCAAAGACAGCAAATACAGAGCCACATCAAAGAATCACCAGACTACGCCACAGACCAGCCCCAACAGGAAACCAGACCGACACACGCGGAGGCAAAAAATAGGAGCCGCGATAAAAAACCACCCGAGCAAGAGGGCAAAAAGCCCGTAACAAGAGCCAGCGCAAACAAAGAAGAGACAGAAGCCATGAAAAAAAGGGAGGCGGGACACGCCAAGGAGAAAGATGTGGTATCCGAACAAGAGGAACACAAAAGGAAAAGCTTAACCACAGAAGAAAACACAAAACAGGCATCCCTACGCAGACGAGACGCAGAAACAGAAGTCAAACGGGAACCCAGCCCCACGAGTAAAAGTAACGGAGAAAAAAAAACCAAACACCCAACAACACAGACAAGCCCCCAACAGAAGAGGATGACAACACAGCACGAAAGGAAAGAAATAAAAAGCGAAGTGGCAATCAAAAGAGAATAGGTAGCACAAAATGGAAAGGACACACACCACCGCACCCGATCAGAACAGATGAAAAGAGAT
		H AACAACGCAGGCCGAAACGATACGCAGCACAAGAAGACCAAAAAAAACAAGCCACAAAGAAGGACACGCAACCAAGGACAACAGGTACAGAACGACACCGAAGGAGAGCCAGGCCAAAGCACAAACCAACCTCAGCTAAACACAGAAACAGCGTATGAAGAAGCGGAGAAAAGAAAGCGCGGTACAAGACCAACCAAACGAGGCAGCAAAAAAATCAAAACAAGAAACAGCAGAAACGGAAAGAAAGCAAGAGACGACAGGAAGGGGGCAACGAGGCCCAACCGGAAAAAAGGTACAGCATCCGGACAAGGAGGACGCGAGAAAAAAGACCTAAGCACAGAAAAGGACACAGAGCGGGCATCCCAACGCGGACCAAACACAAGAGCAGAGATCAAACAGGAACCCGGCCCCACGAGGAGAAACCACAGAACAGGAAAAGCCAAACATCCAAGAACACGAGCAACCCCCACGCAGGAGGAGATGACAGTACAACATGAAAGAGAAGGAACAACAAGCAAAACGGTAATCAGGATAGACTCGGCAGCTCGTGAAGGAGACAGCGCACACCACCGAACCCAATTAGGACGGGCGACCAAAAAT
		
		[Start of d2]
		A ATCCTTGGAATGTATCCGTAGCGCCTGGGCGGTTGCCCGAATCTTGAAGCAGCACAGGCAGCAGTCTGAACGCACGAAGCCGACTGGTGACGAACGCACCTTTCCCCTGGGGCGGTGTAATGATCCGGCAGGGAAGGAGAGAGACGCGCTAAAAACGCGTCTCGTCAGATAACGTCAAGCCCAACGCCTGGGAGGCTCCTCTCATCTACGGGATGGAGTAGTCAGAGGCACTGGGCAGGGATCTCATCCCTCTCGTGCTTGTGATTCCGTGTCTGCGGATGCAAATTCCCAGAAGTCAAACGGTATTCGTATCGTGGACGCCTGTTTATTGGTAAGTGAAGTCCATCACAAGTCTTAGCCTTCCTGAAAGTACTTGATACGATTTGAATAGGATCAAAATACACTAACGAAATACATCTCACATTTGGCGCCTCCATCAAGCTATCTCAGCTGCGTACCTTTCCGCTGCCAGGCAACCAAACCGCGTCTCGTCATCCCACACACGAGTTGCCGGGTGTACGATGTCGGCTTTATTAACGGAAGCCCAAGAGGTATCGGCGTCCAGATACGGTGTGGTACGGCCTGGTTCGCGTCCATGAT
		B TCATATAGGAGGTGCTTAAGTCATGAACAGGGCTGCCAACATGAGATAAATCAGGGTCGTATCGTTGTACTGGCTCTCTCCCCCCAGCAGGGGATAGCGCCTTGACATCGGTCACTCTTATGAATTTACCGTGGCTTTGGCGCGAGCGATGCACCCCGTGCTACCATCTCAATGCACTCCGGAGGGCCAATTAGGTAGGGGCGCCCCGTAACAATCCTCTACGTTATTCAAGGCGAACAGTAGCAGCTCATTCTTCATCCCCAACTTATAAATTGCCTACGGAACGGCCCAAGGAGGTGTAGGAGCATAGTCTAGTACGGTCGTCATACTTAATGCGCTGGGGTCGTAATAATCAAGTATCTTATTCCTGGCTTGAGCCCATGAAAGCCAAACGTGTGATACAAGGGAGCTAGCTTGTCGTCATGAGTTCCGTAGGGTTTGGTTAGACACACGCGCGTACGGTCCATGGTGGAACCCCGCATCCCGAACCCCTGCTTTAAACTCATCATTATAGATAACTAGCGTCTTGAGGACCTACCTCTTGTCCAAACTTCTATGGCTCAATATAATACGGGTTATATATAGCCGGTTGAATTTGAT
		C GCACATAAGTATGCAGGGCATTCATTGCGGGCAGGGGTCAAGTGGTTAGTGTTGGTTGCTGTGAATGTTTCAGACGGCGTACGTTCAGTGGAGCGTGCAAAGTTCATTTAGGGGTACCAAATTCATGTACGGATGCACGTGCACTACGGTGTGTTGCTTCCTTGGCATGTCAGTCTAAACAAGCTCTTCGAATGTAAATAGCTAGGTGATATTACAGACATTAAGACGTAGGATAGAGTATTCTCACGTGTCGTCCCTATCAGGTAGATTAGTCGGTGGTAGCAGCTCTTCACGGTGAGGGTGCTTCTCTCTTGGCGACTGCGCAGCCTTTATAGGGCAGTGAGCCTCTTGCTCTGAACTATGGTAAGCCAACGGCCCGCAACAAAGTAAAGCAAGCAAAACCCGGCCGCATAGTGGACCAACTCTACTATACGTGGCGGTTCGAGGTAGTCGCGCTACCTCTCAGAGGCTGGGACCTTGCTCTCAAGAAATGACTTAATACACACCTTTGCTGTCAGGAGGAAGTAGCCGGGGTGTTGGTACGCACCTATCACCGACGATCCAGGGGGAGGCCGATAGGCATCTACTCTAGAGATTGAG
		D TAGCACAAATACGGCTTCTAATGTTGGCCCACATGCGTCTGAAAGCATGAGATACGCATCTTCCACGTGCACGAATTACCCCCCGATATCTAACTCCATGTTTACAATGGATCATAAATTAATCCCAAATAAATTCGCCTATGAAAGAAATTGCCGCCACCCAGACACACAATGCTAAACATGAGCACAGAATACAGGTTATAAGTCTTGAGTTAGATAATGTGCGTCTATGAAGGCGTCTTCTAATTTGTGCCGTCCGTAAAAGTAGTTGGCCTGTGGATCAAGTGCATAAGCGTGACGTTGCCTATAGCTGATTTATTATGGATTTACAATCCCCCGTCCTCTGTCCTATTTTGATTTGGTCGTACCTAGTGTACCCGGTGAACAAAAAGCATAGATCAGACAAACCGAAGATTCAACTCATCGCCCCAATAAGGCAGCCCGCCGAGTAGGCCACCGTCAGCTACCTAGGGGACATTTAGCATACGGGAGAATTCTGTTTATAGTCGCGCTTTAAGTATGGGACCTGTGGCAGAAGATTGCACACTGACTACCGACGTTCTATAGACGGCGCAGGGAGCCTAAGTACTGTCGTCATCC
		E TCAGAGCACTTCGCTAATTATCGCCGACCGGCATGGATTATACCAGAAGCGTGTGCTAGAAGTCATCTGCGCTTATTGGAACCCGGAAGCGTAACCCATGCGCTTAATGTCTCTAACATCCCCACCGATAAGTTATTCTGGGGTTAGGATTTCTGACGTTTACGGTAATCTGGACGATACAAGCTCAGAGACCGTAATTCTCACGGCGTTACGTATTATTCGCACGTATTCGTCACTACCTTCTCACGATTGTAGGCTATATACTGAAACACCTCACGGCCGAGGTACAGCAGCGTCATGGTCCTATTGGGCGTGTGATTGCGGCGACCATGGTCTGCATGATCTGGACCTCTATGTTCCCCTCTACGCCCACAAAACGGTAGAAATGTTAGCAATCCAACCACCGACGCAATGTCTTACTCTTGGCTTGCCTTCCTAAGTAAACGACGCCGACTGTCGCCCCCCGCTGAAGAAAGAATGCTTACATTCTTTAATTAAGTGAATTCCAACTCAAAGAATGGAGGTGCACCTGGGTACGGGGACATGTATACAGATGGGGTCTCTTTATCGCCATGCTGAGCCTAGACTGGCTCTACGTCG
		F TCCCACCACTAAGCTAACAATAGGCTACCGGCATGAATCCTAACAGAAGCGTCTCCGACAGGGCCTCAGCGCTTCTTGAAACCCGGTAGCTTAACCCATGCCCGGAATGTGTATTACTGCACCCCCGATTAGTTATTCCTGGGAAGGGATTTCTTACTATCATGCAAAACTGCACTCTACCCGGGGATGCAGCGTAAGTCTAACGGCCTTACGGAAAATTCGGCTGCATTCCTCAGCATGTTCTCACAAGTGAAGACTATACACTAGAACATCTAACGGCAGAGTTAAATCACCCTGATGGTCTTCTTGCGCGTGTAATTTCGGCGGCCGTAGTTCGCACGCTCTGGAACTGTATGTTCCCCTGAACCCCCACCCAAAGCCAAAGCTGTTCGTAAGTCAAGCAAAGATACAACGGCTCACACTTGTGATCCCTGGATAATCCGGACTCGCCGACTGTCGTGACCGGCCTGTCAGACAATGCTCATATCCTAATACCATTTTATAATCCTCGCTTGGATTTGAGGAACACCTGGGTCCGGCGATATGTATACAGACCGGTTCTCATAATAGCACTTTTGATCGCAGCCTGCCTCTTGGTCT
		G TTGACGGGATTTGGTGCGCCTGGTCCTCGTGCGGACAATATTACATGTGGTAGTGGTTACATTGGAGTGACTTAACTGCATCCCGTAGAGATGGAGATAGCCTCGTCAGCATGATAATTAAGCTAAACGTCACGGCATGTAGGCGGACATCGAGGCTCTGATTGGGAACCTGTGAGGGTTGCTAACAACGAGGCATCTGACGAGGTGAGAGCGTCGTTACCACTATCGATGGTCCCAAAAGCCTCGAACGCAGATATTAACCACATTGCGGGTTTGCAGGAGAAGGATTCATCTTTTGTGTTCGACGCAGGCTGCTACTGCCGGGCCCTGTTGGCCAAATGCTCAGACCGGATAGATTCATCCGTTGTGATACTCGCCGCAGAACAAGCATTCAAAGGTCAAGCGGTCCCGAATATTCACCGTAAGGTGTAGCGCCCAGCCGCCCACGGAAGAAGGTCGTCAAGCGCCTACTGTACTATTCTTACAACCACTGACTAGCTGACCTCACTACACATTTAGTTGTGAATGCAGGTATAATATTTATCCGGAACTGGCAATTCTGGCAAAGAGCTAGAGCGATCCTTGGCTCTTGACCTAGAT
		H CAGCATGACTTGGTAGCGTCTAGTCATGCGCAGCAGAGCACAACAGACAATGACGCAGTCATGGGAGTGAAGGAATTGGACCCCTTTGAGACGTCGCACGCCTTGTCTGGAGGGTAACTCAGGCCCACGTCTGGTCTCATCGGCTAAAGTGGGTATTCTGCCTGGTAGCCAGTAAAGGTCGGTCCAATAGAGACAAATGGGGTCGTCAGACCCGTGAACGTACTATAGCTGGTCCCGGGACCGACGGGAGTATATTATATTCGCTGTGCCAGTCTTGCTAAGGGGGAAGCATGTCCATCATTGTTCTGAGGCTTCTTCTGTCCGACCTGTGTAATGAAACGCACTTACCGGTTGCTTTCATCGGAGCTTGTACGCCCCCTAATATGCGCGGTCAAAGCTGAAGCGTTCGCGCAGATTCGCCAAGAGATGCCATTCACATGCGAGGATGCAATAAGGTTCTCGACCGCAATGTGTTCTTAGCTTCGCTTCGCGCATTCGCTAGCATGACCCCGCATACAGGCGTTAGTGCTTGTATACTGTGCATCTATTTCAGTCTAAGTTGGAAACGAGAGACAGCAATTAGTAGTTGATAGCCTAAAT
		;
End;

Begin sets;
  charset d1 = 1-600;
  charset d2 = 601-.;
  charpartition genes = gene1:d1, gene2:d2;
End;

Begin assumptions;
  usertype 10_1 = 4  [weights transversions 10 times transitions]
         a  c  g  t
     [a] .  10 1  10
     [c] 10 .  10 1
     [g] 1  10 .  10
     [t] 10 1  10 .
   ;
End;

Begin paup;
  [1] set autoclose=yes;
  [2] hompart partition=genes seed=1;
  [3] include d1/only;
  [4] hsearch;showtree;
  [5] include d2/only;
  [6] hsearch;showtree;
  [7] include all;
  [8] ctype 10_1:d1;
  [9] hompart partition=genes seed=1;
      include d1/only;
      hsearch;showtree;
      include d2/only;
      hsearch;showtree;
End;