1. Phylogenetic trees Tutorial 6

2. Distance based methods UPGMA Neighbor Joining Tools Mega phylogeny.fr DrewTree Phylogenetic Trees

3. a d c b acbd fe Unweighted Pair Group Method using Arithmetic Averages UPGMA Assumption: Divergence of sequences is assumed to occur at constant rate. Therefore the distance to root is equal.

4. In the real world - Divergence of sequences doesn’t occur at constant rate.

5. 5 Neighbor Joining Algorithm Constructs unrooted tree.

6. Step by step summary: 1.Calculate all pairwise distances. 2.Pick two nodes (i and j) for which the relative distance is minimal (lowest). 3.Define a new node (x). 4.Calculate D ix and D jx - the distance of the chosen nodes I and J to the new node X, as well as the distance from X to all other nodes. 5.Continue until two nodes remain – connect with edge. Neighbor Joining (Not assuming equal divergence)

7. A B C D E EDCBA 4139 22-A 4341 --B 2018---C 10----D -----E Step 1. Calculate all pairwise distances.

8. Problem: unrelated sequences approach a fraction of difference expected by chance  The distance measure converges. Jukes-Cantor Measuring Distance

9. Measuring Distance (cont) Euclidean Distance: Given a multiple sequence alignment, calculate the square root of the sum of the score at every position between two sequences the score increases proportionally to the extent of dissimilarity between residues

10. Step 2. Pick two nodes (i and j) for which the relative distance is minimal (lowest). Relative distance between i and j Distance between i and j from the distance table Distance of i from all other sequences Number of leaves (=sequences) left in the tree

11. EDCBA 4139 22-A 4341 --B 2018---C 10----D -----E Step 2. Pick two nodes (i and j) for which the relative distance is minimal (lowest).

12. EDCBA -44 -47.3-74-A -44 -47.3--B -57.3 ---C -64----D -----E A,B is the pair with the minimal M i,j distance. The Mij Table is used only to choose the closest pairs (lowest value) and not for calculating the distances Etc. Step 2. Pick two nodes (i and j) for which the relative distance is minimal (lowest).

13. Step 3. Define a new node (x) A B C D E X

14. Step 4. Calculate D ix and D jx - the distance of the chosen nodes I and J to the new node X, as well as the distance from X to all other nodes. EDCX 3129 -X 2018--C 10---D ----E Now we’ll calculate the distance from X to all other nodes.

15. Step 5 - Continue until two nodes remain New M i,j table EDCX -44 -49-X -44 --C -49---D ----E A B C D E XY

16. New D i,j table EDY 119-Y 10--D ---E Only 2 nodes are left. Let’s calculate all the distances to Z A B C D E XY Z

17. The tree 6 4 E D C 5 9 12 10 B A 20 Z Y X And in newick tree format ((C(D,E))(A,B))

18. Tools and viewers - phylogenetic trees

19. http://www.megasoftware.net/index.html

20. http://www.phylogeny.fr/version2_cgi/one_task.cgi?task_type=phyml

21. e-mail address sequences

25. http://www.phylodiversity.net/rree/drawtree/index.html cladogram phylogram