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.
