NAME

       display_rate_matrix - this tool is part of the PHAST suite

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.