[!Example from Felsenstein's PROTPARS documentation]

[This example demonstrates the use of PAUP to perform an
analysis equivalent to Felsenstein's PROTPARS program from
the PHYLIP package.  Stepmatrices are constructed which
specify the minimum number of amino acid replacements
required to convert one amino acid to another.  (Silent
nucleotide substitutions are "free".)

Note the special treatment for serine, whose codons are not
adjacent in the genetic code.  The two forms of serine are
represented as "1" and "2", and "S" is then treated as an
ambiguity code for these two states.  The "1" and "2" symbols
must therefore be added to the standard protein-format
symbols (the single-letter amino acid codes).  Also, gaps
are treated as additional character states by Felsenstein's
program, hence the "gapmode=newstate", which overrides the
default of "gapmode=missing".

MJS: Nope, I've dropped the gapmode stuff and column/row below
]

begin assumptions;
	usertype protpars = 22
	[This matrix gives the minimum number of amino acid
	replacement substitutions needed to convert one amino
	acid to another, based on the genetic code used in
	nuclear genes of most organisms and chloroplast genes
	in plants).  It was computed using a program written
	by DLS.
	]
	     A C D E F G H I K L M N P Q R 1 2 T V W Y *
	[A]  0 2 1 1 2 1 2 2 2 2 2 2 1 2 2 1 2 1 1 2 2 2
	[C]  2 0 2 2 1 1 2 2 2 2 2 2 2 2 1 1 1 2 2 1 1 1
	[D]  1 2 0 1 2 1 1 2 2 2 2 1 2 2 2 2 2 2 1 2 1 2
	[E]  1 2 1 0 2 1 2 2 1 2 2 2 2 1 2 2 2 2 1 2 2 1
	[F]  2 1 2 2 0 2 2 1 2 1 2 2 2 2 2 1 2 2 1 2 1 2
	[G]  1 1 1 1 2 0 2 2 2 2 2 2 2 2 1 2 1 2 1 1 2 1
	[H]  2 2 1 2 2 2 0 2 2 1 2 1 1 1 1 2 2 2 2 2 1 2
	[I]  2 2 2 2 1 2 2 0 1 1 1 1 2 2 1 2 1 1 1 2 2 2
	[K]  2 2 2 1 2 2 2 1 0 2 1 1 2 1 1 2 2 1 2 2 2 1
	[L]  2 2 2 2 1 2 1 1 2 0 1 2 1 1 1 1 2 2 1 1 2 1
	[M]  2 2 2 2 2 2 2 1 1 1 0 2 2 2 1 2 2 1 1 2 3 2
	[N]  2 2 1 2 2 2 1 1 1 2 2 0 2 2 2 2 1 1 2 3 1 2
	[P]  1 2 2 2 2 2 1 2 2 1 2 2 0 1 1 1 2 1 2 2 2 2
	[Q]  2 2 2 1 2 2 1 2 1 1 2 2 1 0 1 2 2 2 2 2 2 1
	[R]  2 1 2 2 2 1 1 1 1 1 1 2 1 1 0 2 1 1 2 1 2 1
	[1]  1 1 2 2 1 2 2 2 2 1 2 2 1 2 2 0 2 1 2 1 1 1
	[2]  2 1 2 2 2 1 2 1 2 2 2 1 2 2 1 2 0 1 2 2 2 2
	[T]  1 2 2 2 2 2 2 1 1 2 1 1 1 2 1 1 1 0 2 2 2 2
	[V]  1 2 1 1 1 1 2 1 2 1 1 2 2 2 2 2 2 2 0 2 2 2
	[W]  2 1 2 2 2 1 2 2 2 1 2 3 2 2 1 1 2 2 2 0 2 1
	[Y]  2 1 1 2 1 2 1 2 2 2 3 1 2 2 2 1 2 2 2 2 0 1
	[*]  2 1 2 1 2 1 2 2 1 1 2 2 2 1 1 1 2 2 2 1 1 0
	;
	typeset *a = protpars:all;
endblock;