#NEXUS 

BEGIN DATA;
DIMENSIONS  NTAX=33 NCHAR=252;
FORMAT DATATYPE=PROTEIN  SYMBOLS = " 1 2 3 4"  MISSING=? GAP=-  MATCHCHAR=. ;
MATRIX

[Your data matrix here; change NTAX and NCHAR accordingly.]

;
END;

BEGIN ASSUMPTIONS;
    
	
    [Converted from PAM250 amino acid transition matrix of Dayhoff et al. (1978, In Atlas of Protein Sequence 
	Structure, ed. M. O. Dayhoff, Washington, DC: National Biomedical Research Foundation). Because there are 
	negative values in the original PAM250 matrix, the most negative value was set equal to 0 and all other 
	values were increased correspondingly. Scores for transitions to and from gaps were not defined in the 
	original matrix. They have been set equal to the most costly transition (25) defined in the matrix. These
	modifications were made by R. K. Kuzoff]
	
	USERTYPE PAM250 (STEPMATRIX) = 21
	
	      A  C  D  E  F  G  H  I  K  L  M  N  P  Q  R  S  T  V  W  Y  -
	 [A] 15 19 17 17 20 16 18 18 18 19 18 17 16 17 19 16 16 17 23 20 25
	 [C] 19  5 22 22 21 20 20 19 22 23 22 21 20 22 21 17 19 19 25 17 25
	 [D] 17 22 13 14 23 16 16 19 17 21 20 15 18 15 18 17 17 19 24 21 25
	 [E] 17 22 14 13 22 17 16 19 17 20 19 16 18 15 18 17 17 19 24 21 25
	 [F] 20 21 23 22  8 22 19 16 22 15 17 20 22 22 21 20 20 18 17 10 25
	 [G] 16 20 16 17 22 12 19 20 19 21 20 17 17 18 20 16 17 18 24 22 25
	 [H] 18 20 16 16 19 19 11 19 17 19 19 15 17 14 15 18 18 19 20 17 25
	 [I] 18 19 19 19 16 20 19 12 19 15 15 19 19 19 19 18 17 13 22 18 25
	 [K] 18 22 17 17 22 19 17 19 12 20 17 16 18 16 14 17 17 19 20 21 25
	 [L] 19 23 21 20 15 21 19 15 20 11 13 20 20 19 20 20 19 15 19 18 25
	 [M] 18 22 20 19 17 20 19 15 17 13 11 19 19 18 17 19 18 15 21 19 25
	 [N] 17 21 15 16 20 17 15 19 16 20 19 15 17 16 17 16 17 19 21 19 25
	 [P] 16 20 18 18 22 17 17 19 18 20 19 17 11 17 17 16 17 18 23 22 25
	 [Q] 17 22 15 15 22 18 14 19 16 19 18 16 17 13 16 18 18 19 23 21 25
	 [R] 19 21 18 18 21 20 15 19 14 20 17 17 17 16 11 17 18 19 15 21 25
	 [S] 16 17 17 17 20 16 18 18 17 20 19 16 16 18 17 15 16 18 19 20 25
	 [T] 16 19 17 17 20 17 18 17 17 19 18 17 17 18 18 16 14 17 22 20 25
	 [V] 17 19 19 19 18 18 19 13 19 15 15 19 18 19 19 18 17 13 23 19 25
	 [W] 23 25 24 24 17 24 20 22 20 19 21 21 23 23 15 19 22 23  0 17 25
	 [Y] 20 17 21 21 10 22 17 18 21 18 19 19 22 21 21 20 20 19 17  7 25
	 [-] 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25  0
	;

	TYPESET * a  = PAM250: all;
END;