PROGRAM: display_rate_matrix
USAGE: display_rate_matrix [OPTIONS] <model_fname>
OPTIONS:
    -t <t>: Output P(t) = exp(Qt) instead of Q.  Requires t >= 0.  
            Use "-t A" to output a matrix for each branch of the tree.
    -f:     Show equilibrium frequencies as an additional table row.  
            In list node they are shown with first tuple being -.
    -e:     Show "exchangeabilities" instead of raw matrix elements 
            (that is, divide each element by the equilibrium frequency 
            of its column).  Not available with -t.
    -d:     Suppress printing of elements on main diagonal.
    -L:     Format table for typesetting with LATEX.  Incompatible with -l.
    -l:     Show matrix elements as a list rather than as a table.  
            When -t is not specified (rate matrix case), only off-diagonal
            elements will be printed.
    -i:     (For use with -l only) Report whether each substitution is
            a transition or a transversion.
    -z:     (For use with -l) Report elements equal to zero (omitted by 
            default, except with -t).  Implied by -a.
    -S:     (For use with -l)  Assume a symmetric matrix and report half 
            as many lines.  Useful with -e.
    -E:     (for use with -l) Print rates and probabilities 
            in scientific notation (format %e instead of %f).
    -a:     (Requires a model of order 3).  Replace a matrix of codon
            substitution rates with the induced matrix of amino acid
            substitution rates, according to the universal genetic
            code.  See Yang, Nielsen, and Hasegawa, 1998.
    -s:     (For use with -a)  Include stop codons (by default suppressed).
    -M <f>: (For use with -l only; implies -a) Read an amino-acid
            substitution matrix from file <f> and report values from
            this matrix with the induced amino acid substitution rates.
            Matrix should be in the format used by BLAST (as
            produced by the NCBI "pam" program) 
    -N <f>  Like -M but for matrices in the format used by the PAML 
            package for amino acid substitution and rate matrices.
    -A <f>: (For use with -l only and not with -M/-N)  Read alternative
            substitution scores from file <f> and report values in
            output.  File <f> should have three columns: a "from"
            tuple, a "to" tuple, and a real-valued score.
            Substitutions not listed will be given null scores and
            reported as "NA".
    -B <f>  Like -A but compares to rates of a single-nucleotide model 
            (order 1).  File <f> should be a standard tree model (.mod) file.
    -C      Report context-dependent transition/transversion rates, as 
            shown in Tables 2 and 3 of Morton et al., JME 45:227-231, 1997. 
            Requires a model of order 3 with a DNA alphabet.
    -h      Print this help message.