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 i