gonk (go for new peaks) is a R2C2 Smith-Waterman aligner that outputs a list of summed scores
To compile, use make
gonk takes two sequences, populates a score matrix for the alignment, and sums scores parallel to the main diagonal.
Options:
-a First fasta file to align (required)
-b Second fasta file to align (required)
-d Use to exclude the main diagonal (it will be set to zero)
-m Use to output the entire score matrix to stdout
-p Penalty for either gap open or extend (defaults to 25)
-o Output file name (defaults to "SW_PARSE.txt")
To align and do nothing else:
./gonk -a a.fasta -b b.fasta -p 25To align and exclude the main diagonal:
./gonk -a a.fasta -b b.fasta -dTo align and output the entire score matrix to matrix.mat:
./gonk -a a.fasta -b b.fasta -m >matrix.matRun parameters and a timer are piped to stderr
affine does the same thing as gonk, except uses a linear gap penalty as opposed to a constant penalty. This is more widely used, but is slower and isn't necessary for usage in C3POa. Nevertheless, I have included it here in case it needs to be used down the line. The penalty and outfile options are slightly different:
-o Gap open penalty (defaults to 25)
-e Gap extend penalty (defaults to 1)
-out Output file name (defaults to "SW_PARSE.txt")
affine can be built with make affine
You can install gonk with sudo make install
You can remove gonk and affine executables with make clean
