display_rate_matrix(1)
this tool is part of the PHAST suite
Description
DISPLAY_RATE_MATRIX
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.
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-f: |
Show equilibrium frequencies as an additional table row. In list node they are shown with first tuple being -. | |
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-e: |
Show "exchangeabilities" instead of raw matrix elements (that is, divide each element by the equilibrium frequency of its column). Not available with -t. | |
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-d: |
Suppress printing of elements on main diagonal. | |
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-L: |
Format table for typesetting with LATEX. Incompatible with -l. | |
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-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. | |
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-i: |
(For use with -l only) Report whether each substitution is a transition or a transversion. | |
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-z: |
(For use with -l) Report elements equal to zero (omitted by default, except with -t). Implied by -a. | |
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-S: |
(For use with -l) Assume a symmetric matrix and report half as many lines. Useful with -e. | |
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-E: |
(for use with -l) Print rates and probabilities in scientific notation (format %e instead of %f). | |
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-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. | |
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-s: |
(For use with -a) Include stop codons (by default suppressed). | |
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-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.
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-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. | ||
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-h |
Print this help message. |