AlbertLudwigsUniversitat FreiburgFakultat fur Angewandte WissenschaftenInstitut fur Informatik

Prof. Dr. Rolf Backofenhttp://www.bioinf.uni-freiburg.de

Anke Buschanke.busch@informatik.uni-freiburg.de

Exercise to the Lecture

Bioinformatik ISS 2008

Exercise Sheet 4 NEW

until: 10.07.2008

Exercise 1

Find the best multiple alignment for sequences a,b and c using the method of Feng & Doolittle! For thepairwise alignment, use the algorithm of Needleman & Wunsch with the similarity function

s(x,y) ={

1 x = y1 x 6= y

The alignment tree is given by:

{a,b}

a b c

{a,b,c}

The sequences are: a = GCATGb = GGCAGc = CCTGA

Exercise 2

Find the phylogenetic tree of the six sequences a,b,c,d,e, and f using the hierarchical clustering methodUPGMA! You are given the distance matrix D:

Di, j =

a b c d e fa 0 8 8 14 14 24b 0 2 14 14 24c 0 14 14 24d 0 2 24e 0 24f 0