phipack-phi1
Phi test and other tests of recombination
Usage
Phi [{-f | -s | -r}]
Filename
[-t]
AlignmentType
Overview
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]
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).