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.