Man page - phipack-phi(1)

Packages contains this manual

Package:  phipack
apt-get install phipack

Manuals in package:
• phipack-phi(1)
• phipack-ppma_2_bmp(1)
• phipack-profile(1)
Documentations in package:
• phipack

Manual

PHIPACK-PHI

NAME
SYNOPSIS
DESCRIPTION
OPTIONS

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NAME

phipack-phi - PHI test and other tests of recombination

SYNOPSIS

Phi [ -f|-s|-r ] Filename [ -t ] AlignmentType

DESCRIPTION

Input file not specified!!! (use -f |-r|-s)

[-p [#]] [-o] [-v] [-g [#]] [-b [#]]

OPTIONS

	-f : Filename = FASTA format
	-s : Filename = Strict phylip file
	-r : Filename = Relaxed phylip file

-t : AlignmentType = D|A|O where D=DNA

A=AA and O=OTHER [default DNA]

	-p : [#] = PHI permutation test [default = FALSE, #=1000]
	-w : # = Change default window size [default w = 100]
	-o : Report other statistics (NSS and Max Chiˆ2) [default = FALSE]
	-v : Verbose [default = FALSE]
	-g : [i] = Print color (scaled) incompatibility matrix (graph.ppm)

i - Image only (no ticks...) [default = FALSE]

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