NAME

       pbsDecode - Decode a binary encoding of a probabilistic biological sequence

DESCRIPTION

       Decode  a  binary  encoding of a probabilistic biological sequence (PBS).  Outputs a table with a row for
       each position in the sequence and a column for each base, such that the (i,j)th value is the  probability
       of base j at position i.  The same codefile that was used to encode the sequence should be given.

              This program performs the inverse function of pbsEncode.

EXAMPLE

       Decode an encoded ancestral sequence:

              pbsDecode anc.human-mouse.bin mammal.code > anc.human-mouse.probs

       where  "anc.human-mouse.bin"  is  a  binary  encoding  of  an ancestral sequence produced by pbsEncode or
       prequel, and "mammal.code" is a codefile produced by pbsTrain.

OPTIONS

       --start, -s <sidx>

              Decode only the subsequence starting at position <sidx>.  Indexing starts with 1.

       --end, -e <eidx>

              Decode only the subsequence ending at position <eidx>.  Indexing starts with 1.

       --discard-gaps, -G Do not report gaps in the PBS.

       --help, -h

              Produce this help message.