Sample NEXUS format (PAUP and MacClade)

#NEXUS
[! CO1 Data][Comments in brackets are ignored by PAUP, the '!' next to the left bracket 
	makes the comment visible when the file is executed by PAUP ]

 begin data;
 dimensions  ntax=6 nchar=36 [If you do not know the number of characters, use a very large number here, place a 
	'@' as the last character of the last taxon, execute the file, and PAUP will generate an error message of 
	one more than the actual number of characters];
FORMAT     
    MISSING=N    respectcase  
  [Enclose the "equate...  =N" in brackets and re-execute file to produce data matrix in PAUP]
   equate="a=N"     equate="c=N" equate=".=N"     equate="n=N"         
   equate="g=N"     equate="t=N"   equate="I=N" 
   [equate="A=R" equate="G=R"   equate="T=Y" equate="C=Y" ][Allows Transversion Parsimony]
   SYMBOLS="ACGTacgtI" INTERLEAVE  [Don't interleave if using a PIR file or a PHYLIP sequential file] 
   GAP=-;  OPTIONS [IGNOR=INVAR   (this option is not available to ver 4- use exclude constant instead)];  
  matrix
DROMTTGNC  TACTACCCTGCTCTTTCT TTATTATTAGTAAGAAGA
     Dros  TACTATCCTGCTCTTTCT TTATTATTAGTAAGAAGA
 YMU09206  TATTATCCATCCTTAACa cTATTAATTTCTAGAAGA
LUCMTPIEA  TTTTATCCTGCATTAACT TTACTATtagtaagtagt [lower case ignored if using the respectcase format]
 MSQNCATR  TATTACCCCTCTTTAACT CTTCTAATTTCTAGAAGT
     Apis  TACTTTCCCTCATTATTT ATACTTTTATTAAGAAAT   ;
  end;
begin assumptions;
charset begin = 1-5;  [Characters sets (for excluding/including etc). This one is named 'begin']
charset various = 8 10 13-16;
charset first = 1-36\3;   [For amino-acid coding, every third base]
charset second = 2-36\3;
charset third = 3-36\3;
taxset  one = 1 3 5;    [Taxa sets, note taxa may be referred to by number or name]
taxset Diptera = DROMTTGNC LUCMTPIEA MSQNCATR Dros;    end;
begin PAUP;
outgroup Apis; [Automatically roots trees at Apis instead of the first taxon when file is executed]
delete DROMTTGNC  ;  [Automatically excludes taxa or taxa sets]
exclude constant various  third ; [Automatically excludes characters or character sets]

  constraints   both_genera =  ((Dros,DROMTTGNC),(LUCMTPIEA, MSQNCATR)); [Constraint tree, only 
	enforced when ticked in the search box]   end;
begin trees;    uTREE both_genera =  (((2,3),6),(4,5)) [Places tree in memory upon execution];     end; 
	set warnreset=no autoclose=yes;

	[exclude missambig;     ]  [This is for PAUP*]	
	[set crit=parsimony;  [This is for PAUP*]]
	hsearch;
	describe all;
;




This page is maintained by Dave Carmean with an eye towards speed and clarity, and last modified 13 May 1996.  Comments or suggestions are welcomed!    


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