#NEXUS 

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

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

;
END;


BEGIN ASSUMPTIONS;

    [Converted from Blosum62 amino acid transition matrix of Henikoff & Henikoff (1992, PNAS USA 89:10915-10919).
	because there are negative values in the original Blosum62 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 (15) defined in the 
	matrix. These modifications were made by R. K. Kuzoff]

	USERTYPE Blosum62 (STEPMATRIX) = 21
	
	      A  C  D  E  F  G  H  I  K  L  M  N  P  Q  R  S  T  V  W  Y  -
	 [A]  7 11 13 12 13 11 13 12 12 12 12 13 12 12 12 10 11 11 14 13 15
	 [C] 11  2 15 15 13 14 14 12 14 12 12 14 14 14 14 12 12 12 13 13 15
	 [D] 13 15  5  9 14 12 12 14 12 15 14 10 12 11 13 11 12 14 15 14 15
	 [E] 12 15  9  6 14 13 11 14 10 14 13 11 12  9 11 11 12 13 14 13 15
	 [F] 13 13 14 14  5 14 12 11 14 11 11 14 15 14 14 13 13 12 10  8 15
	 [G] 11 14 12 13 14  5 13 15 13 15 14 11 13 13 13 11 13 14 13 14 15
	 [H] 13 14 12 11 12 13  3 14 12 14 13 10 13 11 11 12 13 14 13  9 15
	 [I] 12 12 14 14 11 15 14  7 14  9 10 14 14 14 14 13 12  8 14 12 15
	 [K] 12 14 12 10 14 13 12 14  6 13 12 11 12 10  9 11 12 13 14 13 15
	 [L] 12 12 15 14 11 15 14  9 13  7  9 14 14 13 13 13 12 10 13 12 15
	 [M] 12 12 14 13 11 14 13 10 12  9  6 13 13 11 12 12 12 10 12 12 15
	 [N] 13 14 10 11 14 11 10 14 11 14 13  5 13 11 11 10 11 14 15 13 15
	 [P] 12 14 12 12 15 13 13 14 12 14 13 13  4 12 13 12 12 13 15 14 15
	 [Q] 12 14 11  9 14 13 11 14 10 13 11 11 12  6 10 11 12 13 13 12 15
	 [R] 12 14 13 11 14 13 11 14  9 13 12 11 13 10  6 12 12 14 14 13 15
	 [S] 10 12 11 11 13 11 12 13 11 13 12 10 12 11 12  7 10 13 14 13 15
	 [T] 11 12 12 12 13 13 13 12 12 12 12 11 12 12 12 10  6 11 13 13 15
	 [V] 11 12 14 13 12 14 14  8 13 10 10 14 13 13 14 13 11  7 14 12 15
	 [W] 14 13 15 14 10 13 13 14 14 13 12 15 15 13 14 14 13 14  0  9 15
	 [Y] 13 13 14 13  8 14  9 12 13 12 12 13 14 12 13 13 13 12  9  4 15
	 [-] 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15  0
	;

	TYPESET * a  = Blosum62: all;
END;