The predict executables (predictb and predictb) each fill in
missing data in haplotype sequences. They also can attempt
to correct for recent mutations when used with a prior
recent mutation probability.
The executables are called as follows:
predict[b|g] [-i ] [-s ]
-i : input sequence file name (default: stdin)
-s : input motif file name (default: stdin)
-m : prob of mutation (default: 0)
-c : specifies correction of known sites inferred to be wrong
Both take the same haplotype input, haplotype files described in
README.files. Missing values are denoted by '?', 'X', or 'x' in these
files. They both also take motif files, also described in
README.files, as input. As output, they produce files of the same
haplotypes with values filled in or corrected based on the motif
input.
The difference between the programs is in the algorithms they use to
predict missing sites. predictb uses a local algorithm, in which each
base is predicted based on the most probable motif covering it.
predictg uses a global algorithm in which it finds the most probable
complete parse of each haploid sequence and then fills in all missing
bases based on the one parse.