MSA with Neighbor-Joining

Example Program

Progressive multiple sequence alignment using neighbor joining for building the guide tree.

This code example illustrates a guide tree creation using neighbor-joing

1	#include <seqan/graph.h>
2	#include <iostream>
3
4	using namespace seqan;
5
6	int main() {

Create an artificial distance matrix

7	String<double> mat;
8	fill(mat, 8*8, 0);
9	assignValue(mat, 08+0, 0);assignValue(mat, 08+1, 7);assignValue(mat, 08+2, 8);assignValue(mat, 08+3, 11);
10	assignValue(mat, 08+4, 13);assignValue(mat, 08+5, 16);assignValue(mat, 08+6, 13);assignValue(mat, 08+7, 17);
11	assignValue(mat, 18+0, 7);assignValue(mat, 18+1, 0);assignValue(mat, 18+2, 5);assignValue(mat, 18+3, 8);
12	assignValue(mat, 18+4, 10);assignValue(mat, 18+5, 13);assignValue(mat, 18+6, 10);assignValue(mat, 18+7, 14);
13	assignValue(mat, 28+0, 8);assignValue(mat, 28+1, 5);assignValue(mat, 28+2, 0);assignValue(mat, 28+3, 5);
14	assignValue(mat, 28+4, 7);assignValue(mat, 28+5, 10);assignValue(mat, 28+6, 7);assignValue(mat, 28+7, 11);
15	assignValue(mat, 38+0, 11);assignValue(mat, 38+1, 8);assignValue(mat, 38+2, 5);assignValue(mat, 38+3, 0);
16	assignValue(mat, 38+4, 8);assignValue(mat, 38+5, 11);assignValue(mat, 38+6, 8);assignValue(mat, 38+7, 12);
17	assignValue(mat, 48+0, 13);assignValue(mat, 48+1, 10);assignValue(mat, 48+2, 7);assignValue(mat, 48+3, 8);
18	assignValue(mat, 48+4, 0);assignValue(mat, 48+5, 5);assignValue(mat, 48+6, 6);assignValue(mat, 48+7, 10);
19	assignValue(mat, 58+0, 16);assignValue(mat, 58+1, 13);assignValue(mat, 58+2, 10);assignValue(mat, 58+3, 11);
20	assignValue(mat, 58+4, 5);assignValue(mat, 58+5, 0);assignValue(mat, 58+6, 9);assignValue(mat, 58+7, 13);
21	assignValue(mat, 68+0, 13);assignValue(mat, 68+1, 10);assignValue(mat, 68+2, 7);assignValue(mat, 68+3, 8);
22	assignValue(mat, 68+4, 6);assignValue(mat, 68+5, 9);assignValue(mat, 68+6, 0);assignValue(mat, 68+7, 8);
23	assignValue(mat, 78+0, 17);assignValue(mat, 78+1, 14);assignValue(mat, 78+2, 11);assignValue(mat, 78+3, 12);
24	assignValue(mat, 78+4, 10);assignValue(mat, 78+5, 13);assignValue(mat, 78+6, 8);assignValue(mat, 78+7, 0);

Out-parameter: A guide tree based upon a distance matrix

25	typedef Graph<Tree<double> > TGraph;
26	TGraph njTreeOut;

Neighbor-joining

27	slowNjTree(mat, njTreeOut);

Console output

28	std::cout << njTreeOut << std::endl;
29	typedef Iterator<TGraph, DfsPreorder>::Type TDfsPreorder;
30	TDfsPreorder dfsIt(njTreeOut,getRoot(njTreeOut));
31	std::cout << "Dfs: ";
32	for(;!atEnd(dfsIt);goNext(dfsIt)) {
33	std::cout << *dfsIt << ", ";
34	}
35	std::cout << std::endl;
36	typedef Iterator<TGraph, EdgeIterator>::Type TEdgeIter;
37	TEdgeIter edIt(njTreeOut);
38	std::cout << "Edges: " << std::endl;
39	for(;!atEnd(edIt);goNext(edIt)) {
40	std::cout << sourceVertex(edIt) << " -- " << targetVertex(edIt) << ": Weight = " << getCargo(*edIt) << std::endl;
41	}
42	return 0;
43	}

See

Graph

SeqAn - Sequence Analysis Library - www.seqan.de