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 Chi^2) [default = FALSE]

       -v: Verbose [default = FALSE]

       -g: [i] = Print color (scaled) incompatibility matrix (graph.ppm)

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