MSA with UPGMA

Example Program

MSA with UPGMA

Progressive multiple sequence alignment using UPGMA for building the guide tree

This code example illustrates a guide tree creation using upgma

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, 32);assignValue(mat, 08+2, 48);assignValue(mat, 08+3, 51);
10	assignValue(mat, 08+4, 50);assignValue(mat, 08+5, 48);assignValue(mat, 08+6, 98);assignValue(mat, 08+7, 148);
11	assignValue(mat, 18+0, 32);assignValue(mat, 18+1, 0);assignValue(mat, 18+2, 26);assignValue(mat, 18+3, 34);
12	assignValue(mat, 18+4, 29);assignValue(mat, 18+5, 33);assignValue(mat, 18+6, 84);assignValue(mat, 18+7, 136);
13	assignValue(mat, 28+0, 48);assignValue(mat, 28+1, 26);assignValue(mat, 28+2, 0);assignValue(mat, 28+3, 42);
14	assignValue(mat, 28+4, 44);assignValue(mat, 28+5, 44);assignValue(mat, 28+6, 92);assignValue(mat, 28+7, 152);
15	assignValue(mat, 38+0, 51);assignValue(mat, 38+1, 34);assignValue(mat, 38+2, 42);assignValue(mat, 38+3, 0);
16	assignValue(mat, 38+4, 44);assignValue(mat, 38+5, 38);assignValue(mat, 38+6, 86);assignValue(mat, 38+7, 142);
17	assignValue(mat, 48+0, 50);assignValue(mat, 48+1, 29);assignValue(mat, 48+2, 44);assignValue(mat, 48+3, 44);
18	assignValue(mat, 48+4, 0);assignValue(mat, 48+5, 24);assignValue(mat, 48+6, 89);assignValue(mat, 48+7, 142);
19	assignValue(mat, 58+0, 48);assignValue(mat, 58+1, 33);assignValue(mat, 58+2, 44);assignValue(mat, 58+3, 38);
20	assignValue(mat, 58+4, 24);assignValue(mat, 58+5, 0);assignValue(mat, 58+6, 90);assignValue(mat, 58+7, 142);
21	assignValue(mat, 68+0, 98);assignValue(mat, 68+1, 84);assignValue(mat, 68+2, 92);assignValue(mat, 68+3, 86);
22	assignValue(mat, 68+4, 89);assignValue(mat, 68+5, 90);assignValue(mat, 68+6, 0);assignValue(mat, 68+7, 148);
23	assignValue(mat, 78+0, 148);assignValue(mat, 78+1, 136);assignValue(mat, 78+2, 152);assignValue(mat, 78+3, 142);
24	assignValue(mat, 78+4, 142);assignValue(mat, 78+5, 142);assignValue(mat, 78+6, 148);assignValue(mat, 78+7, 0);

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

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

UPGMA

27	upgmaTree(mat, upgmaTreeOut);

Console output

28	std::cout << upgmaTreeOut << std::endl;
29	// Dfs Iterator
30	typedef Iterator<TGraph, DfsPreorder>::Type TDfsPreorder;
31	TDfsPreorder dfsIt(upgmaTreeOut,getRoot(upgmaTreeOut));
32	std::cout << "Dfs: ";
33	for(;!atEnd(dfsIt);goNext(dfsIt)) {
34	std::cout << *dfsIt << ", ";
35	}
36	std::cout << std::endl;
37	typedef Iterator<TGraph, EdgeIterator>::Type TEdgeIter;
38	TEdgeIter edIt(upgmaTreeOut);
39	std::cout << "Edges: " << std::endl;
40	for(;!atEnd(edIt);goNext(edIt)) {
41	std::cout << sourceVertex(edIt) << " -- " << targetVertex(edIt) << ": Weight = " << getCargo(*edIt) << std::endl;
42	}
43	return 0;
44	}

See

Graph

SeqAn - Sequence Analysis Library - www.seqan.de