.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH RNR-TII "1" "October 2021" "rnr-tii 1.0.1" "User Commands"
.SH NAME
rnr-tii \- computes the taxonomic instability index
.SH DESCRIPTION
This is RnR\-tii version 1.0 released by Andre J. Aberer in 2011\-10\-25.
.PP
This program computes the taxonomic instability index.
.PP
SYNTAX: rnr\-tii \fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h] [\-x <excludeFile>]
.PP
OBLIGATORY:
\fB\-i\fR <bootTrees>
.IP
A collection of bootstrap trees.
.PP
\fB\-n\fR <runId>
.IP
An identifier for this run.
.PP
OPTIONAL
\fB\-z\fR <z>
.IP
The exponent used in the TII formula. Use small values to emphasize close relationships and vice versa. DEFAULT: 2
.PP
\fB\-w\fR <workDir>
.IP
A working directory where output files are created.
.PP
\fB\-x\fR <excludeFile>
.IP
Exclude the taxa in this file (one taxon per line) prior to computing the TII.
.PP
\fB\-h\fR
.IP
This help file.
.SH AUTHOR
This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program.