# Tree construction Problem set

1. Construct a similarity matrix from this alignment:

Seq A G A U C U U U G G A U C Seq B A A U C U C U G G A U U Seq C C A U C U U U - G A U G Seq D A A U C U U U G G A U U Seq E C A U C U C U G A A U G

2. Given the Jukes & Cantor conversion graph, convert the similarity matrix from question 1 to a distance matrix.

3. Given this distance matrix, draw a tree relating these sequences and label the lengths of the branches of the tree:

Seq A Seq B Seq C Seq D Seq A - - - - Seq B 0.2 - - - Seq C 0.6 0.6 - - Seq D 0.9 0.9 0.9 -

4. Given this distance matrix, draw the structure of a tree relating the sequences using the neighbor-joining method, and label the lengths of the branches:

Seq A Seq B Seq C Seq D Seq E Seq F Seq A - - - - - - Seq B 0.2 - - - - - Seq C 0.7 0.7 - - - - Seq D 0.6 0.6 0.5 - - - Seq E 0.7 0.7 0.8 0.7 - - Seq F 0.6 0.6 0.7 0.6 0.3 -

5. Generate a tree from this alignment using the neighbor-joining method, with approximate branch lengths, from these X RNA sequences.

Thiobacillus ferrooxidans GAAUUCCCGGGAG-GGGCCAGGCGACCCCCGAAUUCCCGG Escherichia coli GAAUUCCCGGAAGCAGACCAGACAGUCGCCGAAUUCCCGG Serratia marcescens GAAUUCCCGGAAGUAGACCAGACAGUCACCGAAUUCCCGG Chromatium vinosum GAAUUCCCGGGAG-GGGCCAGACAGUCCCUGAAUUCCCG-