#NEXUS 


BEGIN DATA;
	DIMENSIONS  NTAX=10 NCHAR=13;

[!A small data file about some living vertebrates.  See pp. 13-19 of the MacClade book for a tutorial introduction to MacClade using this file.

Thanks to Hans Sues and Neil Shubin for help in gathering the data.

Note that the character Body Covering might better be considered as evolving according to character state tree, rather than as an unordered character, but this would restrict some aspects of this tutorial.]
	FORMAT SYMBOLS= " 0 1 2 3 4" MISSING=? GAP=- ;
	CHARSTATELABELS  
		1  amnion / absent present,
  2  appendages / fins legs_only 'legs+wings',
  3  body_covering / derm.scales smooth epid.scales feathers hair,
  4  thermoreg. / poikilotherm homeotherm,
  5  int.nostrils / absent present,
  6  atrial_septum / absent present,
  7  temp.fenestrae / none one two,
  8  hemipenes / absent present,
  9  suspensorium / not_strep. streptosylous,
  10  gizzard / absent present,
  11  antorb_fenes / absent present,
  12  lat.sphen / ossified not,
  13  teeth / not_ped. pedicillate
		;

MATRIX
[                          10  ]
[                          .   ]

rayfinned_fish    00000000?0010
frogs             0110110000011
turtles           1120110000010
lungfish          00001100?0010
salamanders       0110110000011
crocodiles        1120112001100
lizards           1120112110010
birds             1231112001100
mammals           1{12}41111000010
snakes            1?20112110010
;
END;


BEGIN ASSUMPTIONS;
	OPTIONS  DEFTYPE=unord PolyTcount=MINSTEPS ;
	TYPESET  bad  = unord: 1-5, ord: 6-13;
	TYPESET * UNTITLED  = unord: 1 3-6 8-13, ord: 2 7;
END;


BEGIN TREES; 

	TRANSLATE
		1	rayfinned_fish,
		2	frogs,
		3	turtles,
		4	lungfish,
		5	salamanders,
		6	crocodiles,
		7	lizards,
		8	birds,
		9	mammals,
		10	snakes
	;
	TREE  * Bad_Guess =  [&R] (1,((5,(10,6)),((9,(7,3)),((2,8),4))));
	TREE Another_Guess =  [&R] (1,(5,(((9,(7,3)),(10,6)),(8,(2,4)))));

END;


BEGIN PAUP;


	constraints herps = ((frogs,turtles,salamanders,crocodiles,lizards,snakes));
	constraints amniotes = ((turtles,crocodiles,lizards,birds,mammals,snakes));
	constraints reptiles = ((turtles,crocodiles,lizards,snakes));
	constraints archosaurs = ((crocodiles,birds));
	constraints homeotherms = ((birds, mammals));
	constraints homrept = ((birds, mammals),(turtles,crocodiles,lizards,snakes));
END;


BEGIN MacClade;
	Version 4.0  81;
	LastModified -1225616331;
	FileSettings editor  '0' '0' '1' '1';
	Singles 100;
	Editor 0001101111111110010001001 '0' '72' Geneva '9' '100' '1' all;
	EditorPosition  '57' '38' '275' '579';
	TreeWindowPosition  '40' '2' '728' '1018';
	ListWindow Characters closed Geneva '9' '50' '10' '265' '352' 000;
	ListWindow Taxa closed Geneva '9' '50' '10' '217' '278' 100;
	ListWindow Trees closed Geneva '9' '50' '10' '276' '490' ;
	ListWindow TypeSets closed Geneva '9' '50' '10' '276' '490' ;
	ListWindow WtSets closed Geneva '9' '50' '10' '276' '490' ;
	ListWindow ExSets closed Geneva '9' '50' '10' '276' '490' ;
	ListWindow CharSets closed Geneva '9' '50' '10' '276' '490' ;
	ListWindow TaxSets closed Geneva '9' '50' '10' '276' '490' ;
	ListWindow CharPartitions closed Geneva '9' '50' '10' '276' '490' ;
	ListWindow CharPartNames closed Geneva '9' '50' '10' '276' '490' ;
	ListWindow WtSets closed Geneva '9' '50' '10' '276' '490' ;
	ChartWindowPosition  '50' '30' '688' '964';
	StateNamesSymbols closed Geneva '9' '10' '50' '30' '148' '220';
	WindowOrder  Data;
	OtherSymbols &/ 00 ?-;
	Correlation  '0' '0' '1000' '0' '0' 10011010;
	Salmo 00000001;
	EditorFile  '2';
	ExportHTML _ MOSS  '100' 110000;
	PrettyPrint 10;
	EditorToolsPosition  '362' '27' '115' '165';
	TreeToolsPosition  '607' '5' '126' '138';
	TreeWindowProgram 10;
	TreeWindow 0000;
	Continuous  '0' '3' 1;
	Calculations 0000001;
	SummaryMode  '0' '0' 0;
	Charts  Geneva '9' (normal) 0010;
	NexusOptions  '0' '0' '50' 001011001;
	TipLabel  '1';
	TreeFont  Geneva '9' (normal);
	TreeShape  1.0 1.0 0100;
	TraceLabels 0101;
	ChartColors  '0' '0' '-1' '9' '0' 1;
	ChartBiggestSpot 1;
	ChartPercent 10;
	ChartBarWidth  '10' 1;
	ChartVerticalAxis 10101;
	ChartMinMax  '0';
	TraceAllChangesDisplay  '1' 1;
	BarsOnBranchesDisplay  '0' '0' '-5536' '10000' '10000' '10000' '10000' '-5536' '-536' '-536' '-536' '6' '1' 0000101;
	ContinuousBranchLabels 0;
	AllStatesBranchLabels 1;
	IndexNotation  '2' 1;
	PrintTree  10.00 '2' '2' '2' '2' '2' '2' '2' '2' '2' '2' '2' Geneva '9' (normal) Geneva '10' (normal) Geneva '9' (normal) Geneva '9' (normal) Geneva '9' (bold ) Geneva '9' (normal) Geneva '9' (normal) '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '1' '1' '1' '1' '0' '1954' '-39' '4' '-40' '0' '1' '2' '1' '8' '0' '0' '0' '2' 1000111000000000000100000111000;
	MatchChar 00 .;
	EntryInterpretation 01;
	ColorOptions 0;
	TreeTools  '0' '5' '4' '0' '10' '4' '0' 00100111111101110;
	EditorTools  '0' '0' '0' '1000' '0' '0' '6' '3' '0' 100000101110001;
	PairAlign  '2' '2' '3' '2' '1' '1' '2' '1' '3' 1010;
	BothTools  '1';
END;