Phylogenetic Trees Tutorial 6. Measuring distance Bottom-up algorithm (Neighbor Joining) –Distance based algorithm –Relative distance based Phylogenetic.

Slides:

Advertisements

Similar presentations

Computing a tree Genome 559: Introduction to Statistical and Computational Genomics Prof. James H. Thomas.

Advertisements

Phylogenetic Tree A Phylogeny (Phylogenetic tree) or Evolutionary tree represents the evolutionary relationships among a set of organisms or groups of.

. Class 9: Phylogenetic Trees. The Tree of Life Evolution u Many theories of evolution u Basic idea: l speciation events lead to creation of different.

Computing a tree Genome 559: Introduction to Statistical and Computational Genomics Prof. James H. Thomas.

Lecture 13 CS5661 Phylogenetics Motivation Concepts Algorithms.

Brandon Andrews CS6030.  What is a phylogenetic tree?  Goals in a phylogenetic tree generator  Distance based method  Fitch-Margoliash Method Example.

Phylogenetics - Distance-Based Methods CIS 667 March 11, 2204.

Phylogenetic trees Sushmita Roy BMI/CS 576 Sep 23 rd, 2014.

UPGMA Algorithm.  Main idea: Group the taxa into clusters and repeatedly merge the closest two clusters until one cluster remains  Algorithm  Add a.

Lecture 7 – Algorithmic Approaches Justification: Any estimate of a phylogenetic tree has a large variance. Therefore, any tree that we can demonstrate.

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Phylogenetic Reconstruction: Distance Matrix Methods Anders Gorm Pedersen Molecular Evolution Group Center for.

. Computational Genomics 5a Distance Based Trees Reconstruction (cont.) Modified by Benny Chor, from slides by Shlomo Moran and Ydo Wexler (IIT)

Branch and Bound Similar to backtracking in generating a search tree and looking for one or more solutions Different in that the “objective” is constrained.

Building phylogenetic trees Jurgen Mourik & Richard Vogelaars Utrecht University.

Distance methods. UPGMA: similar to hierarchical clustering but not additive Neighbor-joining: more sophisticated and additive What is additivity?

The Tree of Life From Ernst Haeckel, 1891.

. Multiple Sequence Alignment Tutorial #4 © Ilan Gronau.

CISC667, F05, Lec15, Liao1 CISC 667 Intro to Bioinformatics (Fall 2005) Phylogenetic Trees (II) Distance-based methods.

. Multiple Sequence Alignment Tutorial #4 © Ilan Gronau.

07/05/2004 Evolution/Phylogeny Introduction to Bioinformatics MNW2.

Multiple sequence alignment

. Class 9: Phylogenetic Trees. The Tree of Life D’après Ernst Haeckel, 1891.

Phylogenetic Trees Tutorial 6. Measuring distance Bottom-up algorithm (Neighbor Joining) –Distance based algorithm –Relative distance based Phylogenetic.

Distance-Based Phylogenetic Reconstruction Tutorial #8 © Ilan Gronau, edited by Itai Sharon.

Building Phylogenies Distance-Based Methods. Methods Distance-based Parsimony Maximum likelihood.

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Distance Matrix Methods Anders Gorm Pedersen Molecular Evolution Group Center for Biological Sequence Analysis.

. Multiple Sequence Alignment Tutorial #4 © Ilan Gronau.

Phylogenetic trees Tutorial 6. Distance based methods UPGMA Neighbor Joining Tools Mega phylogeny.fr DrewTree Phylogenetic Trees.

Phylogenetic trees Sushmita Roy BMI/CS 576

Multiple Sequence Alignment S 1 = AGGTC S 2 = GTTCG S 3 = TGAAC Possible alignment A-TA-T GGGGGG G--G-- TTATTA -TA-TA CCCCCC -G--G- AG-AG- GTTGTT GTGGTG.

Chapter 9 Superposition and Dynamic Programming 1 Chapter 9 Superposition and dynamic programming Most methods for comparing structures use some sorts.

Molecular evidence for endosymbiosis Perform blastp to investigate sequence similarity among domains of life Found yeast nuclear genes exhibit more sequence.

1 Summary on similarity search or Why do we care about far homologies ? A protein from a new pathogenic bacteria. We have no idea what it does A protein.

Phylogenetic Analysis. General comments on phylogenetics Phylogenetics is the branch of biology that deals with evolutionary relatedness Uses some measure.

BINF6201/8201 Molecular phylogenetic methods

Taking the Bite (Byte?) Out of Phylogeny Jennifer Galovich Lucy Kluckhohn Jones Holly Pinkart.

OUTLINE Phylogeny UPGMA Neighbor Joining Method Phylogeny Understanding life through time, over long periods of past time, the connections between all.

Phylogenetic Prediction Lecture II by Clarke S. Arnold March 19, 2002.

Phylogenetic Trees Tutorial 5. Agenda How to construct a tree using Neighbor Joining algorithm Phylogeny.fr tool Cool story of the day: Horizontal gene.

Phylogenetic Trees  Importance of phylogenetic trees  What is the phylogenetic analysis  Example of cladistics  Assumptions in cladistics  Frequently.

Building phylogenetic trees. Contents Phylogeny Phylogenetic trees How to make a phylogenetic tree from pairwise distances  UPGMA method (+ an example)

Introduction to Phylogenetics

Calculating branch lengths from distances. ABC A B C----- a b c.

Using Traveling Salesman Problem Algorithms to Determine Multiple Sequence Alignment Orders Weiwei Zhong.

Using traveling salesman problem algorithms for evolutionary tree construction Chantal Korostensky and Gaston H. Gonnet Presentation by: Ben Snider.

Algorithms in Computational Biology11Department of Mathematics & Computer Science Algorithms in Computational Biology Building Phylogenetic Trees.

Molecular Phylogeny. 2 Phylogeny is the inference of evolutionary relationships. Traditionally, phylogeny relied on the comparison of morphological features.

Phylogenetic Analysis Gabor T. Marth Department of Biology, Boston College BI420 – Introduction to Bioinformatics Figures from Higgs & Attwood.

Phylogeny Ch. 7 & 8.

Phylogenetic trees Sushmita Roy BMI/CS 576 Sep 23 rd, 2014.

Tutorial 5 Phylogenetic Trees.

1 CAP5510 – Bioinformatics Phylogeny Tamer Kahveci CISE Department University of Florida.

Distance-Based Approaches to Inferring Phylogenetic Trees BMI/CS 576 Colin Dewey Fall 2010.

Distance-based methods for phylogenetic tree reconstruction Colin Dewey BMI/CS 576 Fall 2015.

Fitch-Margoliash Algorithm 1.From the distance matrix find the closest pair, e.g., A & B 2.Treat the rest of the sequences as a single composite sequence.

Phylogenetic trees. 2 Phylogeny is the inference of evolutionary relationships. Traditionally, phylogeny relied on the comparison of morphological features.

Taking the Bite (Byte?) Out of Phylogeny Jennifer Galovich Lucy Kluckhohn Jones Holly Pinkart.

Lecture 14 CS5661 Neighbor Joining Generates unrooted tree, allowing for unequal branches Given: Distance matrix for sequences Steps: Repeat 1-3 till all.

Multiple Sequence alignment and Phylogenetic trees.

Inferring a phylogeny is an estimation procedure.

Clustering methods Tree building methods for distance-based trees

Multiple Sequence Alignment

Motif discovery and Phylogenetic trees.

Phylogenetic Trees.

Multiple Sequence Alignment

Lecture 7 – Algorithmic Approaches

Presentation transcript:

Phylogenetic Trees Tutorial 6

Measuring distance Bottom-up algorithm (Neighbor Joining) –Distance based algorithm –Relative distance based Phylogenetic Trees Tutorial 6

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

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

Star Structure Assumption: Divergence of sequences is assumed to occur at constant rate  Distance to root equals a d c b

6 abcd a0875 b8039 c7308 d5980 a d c b Basic Algorithm Initial star diagramDistance matrix

7 abcd a0875 b8039 c7308 d5980 a d c b Choose the nodes with the shortest distance and fuse them. Selection step

8 a d c,b e a a,d c e b D ce D de f d a c e b D af D de f D ce D bf abcd a0875 b8039 c7308 d

9 Neighbor Joining Algorithm Constructs unrooted tree.

Step by step summary: 1.Calculate all pairwise distances. 2.Pick two nodes (i and j) for which the distance is minimal. 3.Define a new node (x) and re-calculate the distances from the free nodes to the new node. 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’ (merging close sequences – not the actual algorithm)

Pick two nodes for which the distance is minimal (i,j)

Node 10 is a new node. 5,6

Re-calculate the distances from new node I,j : the fused nodes (5,6) X :a new added node (node 10) m :the remaining nodes in the star

Calculate D ix and D jx r : ~average distance to nodes L : number of leaves left in the tree (leaves nodes representing taxa, sequences,etc)

Calculate Dix and Djx r 5 =ΣD 5k /(L-2)= /(9-2)= r 6 =ΣD 6k /(L-2)= /(9-2)= ΣD 5k ΣD 6k

Calculate Dix and Djx D 10,5 =(D 5,6 +r 5 -r 6 )/2=( )/2) = D 10,6 =D 5,6 -D 10,5 = =

Step

Step

Step 4

Step 5

Step 6

Step 7

Problems

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) and re-calculate the distances from the free nodes to the new node. 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)

Step 2. Pick two nodes (i and j) for which the relative distance is minimal (lowest).

Negative values As the average distance from the common ancestor to the rest of the nodes increases, M ij has a lower value. Select pair that produce lowest value Reevaluate M with every iteration J I X M

Re-calculate the distances from new node J I X M

31 EXAMPLE A B C D E B 5 C 4 7 D E F A B C D E B -13 C -11 D E F Original distance MatrixRelative Distance Matrix (Mij) The Mij Table is used only to choose the closest pairs and not for calculating the distances

Bacillus E.coli Pseudomonas Salmonella Aeromonas Lechevaliera Burkholderias Problems with phylogenetic trees

Software PHYLIP PAUP MEGA More