.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
.TH CAI "1" "October 2022" "CAI 1.0.2" "User Commands"
.SH NAME
CAI \- calculate codon adaptation index for a DNA sequence
.SH SYNOPSIS
.B CAI
[\fI\,OPTIONS\/\fR]
.SH OPTIONS
.TP
\fB\-s\fR, \fB\-\-sequence\fR FILE
The sequence to calculate the CAI for.
[required]
.TP
\fB\-r\fR, \fB\-\-reference\fR FILE
The reference sequences to calculate CAI
against.  [required]
.TP
\fB\-g\fR, \fB\-\-genetic\-code\fR INTEGER
The genetic code to use. Defaults to 11.
.TP
\fB\-\-help\fR
Show this message and exit.