.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.12.
.TH PHIPACK-PHI "1" "August 2020" "phipack-phi 0.0.20160614" "User Commands"
.SH NAME
phipack-phi \- PHI test and other tests of recombination
.SH SYNOPSIS
.B Phi
[\fI\,-f|-s|-r\/\fR] \fI\,Filename  \/\fR[\fI\,-t\/\fR] \fI\,AlignmentType\/\fR
.SH DESCRIPTION
Input file not specified!!! (use \fB\-f\fR|\-r|\-s)
.IP
[\-p [#]] [\-o] [\-v] [\-g [#]] [\-b [#]]
.SH OPTIONS
.HP
\fB\-f\fR: Filename = FASTA format
.HP
\fB\-s\fR: Filename = Strict phylip file
.HP
\fB\-r\fR: Filename = Relaxed phylip file
.TP
\fB\-t\fR: AlignmentType = D|A|O where D=DNA
A=AA and O=OTHER [default DNA]
.HP
\fB\-p\fR: [#] = PHI permutation test [default = FALSE, #=1000]
.HP
\fB\-w\fR: # = Change default window size [default w = 100]
.HP
\fB\-o\fR: Report other statistics (NSS and Max Chi^2) [default = FALSE]
.HP
\fB\-v\fR: Verbose [default = FALSE]
.HP
\fB\-g\fR: [i] = Print color (scaled) incompatibility matrix (graph.ppm)
.IP
i \- Image only (no ticks...) [default = FALSE]