---
name: "display_rate_matrix"
section: "1"
platform: "linux"
package: "phast"
version: "1.7+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/display_rate_matrix"
---

# display\_rate\_matrix(1)

this tool is part of the PHAST suite

## 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.