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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH MAKEHKY "1" "May 2016" "makeHKY 1.4" "User Commands"
.SH NAME
makeHKY \- Generates an HKY tree model, given kappa (the transition/transversion
.SH 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.
.SH OPTIONS
.HP
\fB\-\-gc\fR, \fB\-g\fR <val>
.IP
Define base composition according to specified G+C composition,
assuming P(A)=P(T) and P(C)=P(G). Default is 0.4.
.HP
\fB\-\-pi\fR, \fB\-p\fR <pi_A,pi_C,pi_G,pi_T>
Override \fB\-\-gc\fR and define base composition explicitly.
Values will
be renormalized to ensure they sum exactly to one.
.HP
\fB\-\-branch\-length\fR, \fB\-t\fR <val>
.IP
Assume a tree consisting of a single branch of specified length.
Default value is 1.
.HP
\fB\-\-tree\fR, \fB\-T\fR <tree.nh>
Override \fB\-\-branch\-length\fR and use specified tree.
.HP
\fB\-\-help\fR, \fB\-h\fR
.IP
Display this help message and exit.
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