Simple NW Alignment Tool

A simple C++ implementation of the Needleman-Wunsch algorithm.

Usage

./Alignment input_sequence1 input_sequence2 output_result output_profile_1 output_profile_2 step_1 step_2 window_length filter_threshold

• input_sequence1, file, input, containing the first sequence;
• input_sequence2, file, input, containing the second sequence;
• output_result, file, main output, has 3 columns;
• output_profile_1, file, output, has 1 column;
• output_profile_2, file, output, has 1 column;
• step_1, int, input, step size 1;
• step_2, int, input, step size 2;
• window_length, int, input, window size;
• filter_threshold, int, input, filter threshold;

Example

With input data from the data folder, run ./Alignment data/input1 data/input2 output1 output2 output3 1 1 100 0. Check that the output files (output1, output2 and output3) match those in the data folder.

Previous Version

The four integer parameters were part of the first input file as shown in the data_ott folder