табуляция = 2 пробела

#include <iostream>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <algorithm>

#include "DataReader.h"

#define DEBUG

void PrintWay(int** way, int i, int j, std::string &seq1, std::string &seq2, 
							std::string &result1, std::string &result2
) {
	if (i < 1 || j < 1) {
		while (i) {
			i--;
			result2.insert(0, 1, seq2[i]);
			result1.insert(0, 1, ' ');
		}
		while (j) {
			j--;
			result2.insert(0, 1, ' ');
			result1.insert(0, 1, seq1[j]);
		}
		return;
	}
	//std::cout << i << ' ' << j << std::endl;
	if (way[i][j] == 1) { i--; j--; result1.insert(0, 1, seq1[j]); result2.insert(0, 1, seq2[i]);  }
	else if (way[i][j] == 2) { i--; result1.insert(0, 1, '-'); result2.insert(0, 1, seq2[i]);  }
	else { j--; result1.insert(0, 1, seq1[j]); result2.insert(0, 1, '-');  }
	PrintWay(way, i, j, seq1, seq2, result1, result2);
}

int main(int argc, char** argv) {
	if (argc < 4) {
		std::cout << "Need more arguments!" << std::endl;
		return 0;
	}
	//Входные данные
	std::string name1, name2, seq1, seq2, alphabet;
	int index_array[128];
	int** score_matrix = ReadData(name1, seq1, name2, seq2, alphabet, index_array, 
																argv[1], argv[2]);
	//Последний аргумент - штраф за вставку/удаление------------------------------
	int penalty = atoi(argv[3]);
#ifdef DEBUG
	std::cout << name1 << std::endl << seq1 << std::endl;
	std::cout << name2 << std::endl << seq2 << std::endl;
	std::cout << ">alphabet" << std::endl << alphabet << std::endl;
	std::cout << ">score matrix" << std::endl;
	for (int i = 0; i < alphabet.length(); i++) {
		for (int j = 0; j < alphabet.length(); j++) {
			std::cout << score_matrix[i][j] << " ";
		}
		std::cout << std::endl;
	}
	std::cout << ">penalty" << std::endl << penalty << std::endl << std::endl;
#endif
	//Алгоритм====================================================================
	int** score = new int* [seq2.length() + 1];
	int** way = new int* [seq2.length() + 1];
	for (int i = 0; i < seq2.length() + 1; i++) {
		score[i] = new int [seq1.length() + 1];
		way[i] = new int [seq1.length() + 1];
		memset(score[i], 0, sizeof(int)*(seq1.length() + 1));
		memset(way[i], 0, sizeof(int)*(seq1.length() + 1));
	}
	for (int i = 1; i < seq2.length() + 1; i++) {
		for (int j = 1; j < seq1.length() + 1; j++) {
			//оставить все как есть
			int way1 = score[i-1][j-1] + 
				score_matrix[ index_array[seq2[i-1]] ][ index_array[seq1[j-1]] ];
			//порвать seq1
			int way2 = score[i-1][j] + penalty;
			//порвать seq2
			int way3 = score[i][j-1] + penalty;
			//выбираем максимум
			if (way1 >= way2 && way1 >= way3) {
				score[i][j] = way1;
				way[i][j] = 1;
			} else if (way2 >= way1 && way2 >= way3) {
				score[i][j] = way2;
				way[i][j] = 2;
			} else {
				score[i][j] = way3;
				way[i][j] = 3;
			}
		}
	}
#ifdef DEBUG
	for (int i = 0; i < seq2.length() + 1; i++) {
		for (int j = 0; j < seq1.length() + 1; j++) {
			std::cout.width(4);
			std::cout << score[i][j] << ' ';
		}
		std::cout << std::endl;
	}
	std::cout << std::endl;
	for (int i = 0; i < seq2.length() + 1; i++) {
		for (int j = 0; j < seq1.length() + 1; j++) {
			std::cout << way[i][j] << ' ';
		}
		std::cout << std::endl;
	}
	std::cout << std::endl;
#endif
	std::string result1, result2;
	int max_score = score[seq2.length()][0], finish = 0;
	for (int j = 1; j <= seq1.length(); j++) {
		if (score[seq2.length()][j] > max_score) {
			max_score = score[seq2.length()][j];
			finish = j;
		}
	}
	PrintWay(way, seq2.length(), finish, seq1, seq2, result1, result2);
	result1.insert(result1.length(), seq1, finish, seq1.length());
	std::cout << result1 << std::endl;
	std::cout << result2 << std::endl;
	std::cout << std::endl << ">score" << std::endl;
	std::cout << max_score << std::endl;
	//Конец=======================================================================
	for (int i = 0; i < alphabet.length(); i++) {
		delete[] score_matrix[i];
	}
	for (int i = 0; i < seq2.length() + 1; i++) {
		delete[] score[i];
		delete[] way[i];
	}
	delete[] score_matrix;
	delete[] score;
	delete[] way;
	return 0;
}