Usage instructions

bra

Usage:
   bra [options] <infile>
 
Options:
        e <float>        Cost of extending a gap (default: 1.0)
        g <float>        Cost of opening a gap (1.0)
        s <float>        Substitution cost (1.0)
        m <int>  Max gap size (1 -- 15)
        u        This help text
        v        Version information
 
Exit codes:
        0        No problem
        1        Could not open input file
        2        Cannot interpret commandline
        3        Error during alignment initialization
        4        Error during alignment computation
        5        Backtracking error
        6        Out of memory
 
Input is given as a FASTA flatfile of sequences. If <infile> is
'--', the input is read from STDIN. The sequences can contain any
8-bit characters, but avoid dashes since they will be used for the
alignment.
 
Output, all pairwise alignments in SELEX format, is written to stdout.

mcbra

Usage:
   mcbra [options] <mother file> <child file>
 
Options:
        e <float>        Cost of extending a deletion (default: 1.0)
        g <float>        Cost of starting a deletion  (1.0)
        d <float>        Cost of a duplication (1.0)
        s <float>        Substitution cost (1.0)
        u        This help text
        v        Version information
 
Exit codes:
        0        No problem
        1        Could not open input file
        2        Cannot interpret commandline
        3        Error during alignment initialization
        4        Error during alignment computation
        5        Backtracking error
        6        Out of memory
 
Input is given using two Fasta flatfiles containing sequences. The
first file contains sequences from a mother/an ancestor, and the
second contains sequences from progreny. The sequences can contain any
8-bit characters, but avoid dashes since they will be used for the
alignment.
 
Output, all pairwise alignments (in SELEX format) with one mother
sequence and one child sequence, is written to stdout.