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

# makeHKY(1)

Generates an HKY tree model, given kappa (the transition/transversion

## NAME

makeHKY - Generates an HKY tree model, given kappa (the transition/transversion

## DESCRIPTION

Generates an HKY tree model, given kappa (the transition/transversion rate ratio).  The equilibrium base composition and either a branch length or a complete tree can be specified by the options described below.

## OPTIONS

**--gc**, **-g** \<val\>

-

  Define base composition according to specified G+C composition, assuming P(A)=P(T) and P(C)=P(G).  Default is 0.4.

**--pi**, **-p** \<pi\_A,pi\_C,pi\_G,pi\_T\> Override **--gc** and define base composition explicitly. Values will be renormalized to ensure they sum exactly to one.

**--branch-length**, **-t** \<val\>

-

  Assume a tree consisting of a single branch of specified length. Default value is 1.

**--tree**, **-T** \<tree.nh\> Override **--branch-length** and use specified tree.

**--help**, **-h**

-

  Display this help message and exit.