phipack-profile(1)

PHI test and other tests of recombination

Section 1 phipack bookworm source

Description

phipack-profile - PHI test and other tests of recombination

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

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

[-w #] [-k #] [- v] [-n #] [-m #]

	-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]

	-w: # = Change default window size for PHI [default w = 100]
	-v: Verbose [default = FALSE]
	-n: # = Change scanning size for regions to test [default n = 1000]
	-m: # = Step size for profile method [default m = 25]