NAME

       phipack-profile - PHI test and other tests of recombination

SYNOPSIS

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

DESCRIPTION

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

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

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]

       -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]