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Find branch lengths between i and j by treating remaining sequences as composite ... I and II are closest neighbors at distance 10. Question: Which of them is closer ...
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Phenetic Approach : Clustering approach, Fitch-Margoliash method, Neighbor-joining method ... Fitch-Margoliash (FM) Algorithm-I ... Fitch-Margoliash Algorithm-II ...
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Fitch-Margoliash. Character Based & Criterion Based Method. Maximum Likelihood. UPGMA ... Fitch- Margoliash. This method modifies WPGMA in branch length determination. ...
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1967 'Construction of Phylogenetic Trees' Fitch & Margoliash. ... 1983 IBM-XT HARD disk (10 Mbytes) 1984 MacIntosh : graphic/mouse interface ...
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Patterns: A.EM, ACAD.MIA. The two patterns 'align' residue E in X differently ... neighbour-joining or Fitch-Margoliash. Un-aligned homologous. sequences ...
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Fitch-Margoliash algorithm for calculating the branch lengths ... 3. Adjust the position of the common ancestor node for A and B so that the ...
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Predicci n de rboles filogen ticos: UPGMA Marco Antonio Robles Montoya
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G53BIO - Bioinformatics Phylogenetic Trees Dr. Jaume Bacardit Prof. Natalio Krasnogor http://www.cs.nott.ac.uk/~jqb/G53BIO Examples from D.A.Krane & M.L. Raymer s ...
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Corona-Viruses. From 'Characterization of a Novel Coronavirus Associated with Severe Acute ... that accurately represents the evolutionary history of the taxa. ...
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Tree length formula as a function of average distances. ... If no swap improves length of the tree, stop and return the tree, else perform ...
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Title: IDEF 1X Concept AND ERwin Operation Author: liubin Last modified by: Created Date: 7/27/1999 4:38:49 PM Document presentation format
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Le seul moyen de de faire une m thode instructive et naturelle, ... Georges Leclerc de Buffon, naturaliste et crivain, Histoire naturelle,1749. ...
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Developed by Willi Henning (Grundz ge einer Theorie der Phylogenetischen ... fitch/kitsch. drawtree/drawgram. Maximum Parsimony. Most common method ...
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Population Genetics Population: group of individuals of the same species. Concept of gene pool. Analyses the amount and distribution of genetic
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Simply counting the number of differences (p distance) may underestimate the ... the most general model for the data - akin to sampling coloured beads from a jar ...
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Evolution What causes evolution? Speciation & hybridization. Uncovering evolutionary history.
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Phylogenetic Tree Construction Methods and Programs
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... 6 2 Aquifex - 4 Deinococc 0.30689 - 5 Thermus 0.21346 0.19106 - 6 Bacillus 0.24745 0.21751 0.22221 - Note that the JC distances ...
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d(AB)C / 2. B. C. step 1 step 2. UPGMA example. Lecture #6 Page 19 ... that other methods (e.g. minimum evolution) will evaluate to find the best tree. Exercises ...
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No transfer of genetic information by ... Algorithm choice is a contested, active research field. ... Order of input can be problematic. Jumble them! ...
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Tree searching (heuristic search) Models (using Modeltest to choose one) ... Use 'hill climbing' methods. Initial tree starts the process, then we seek to ...
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Title: Wat is taalkunde? Author: Henriette de Swart Last modified by: de Swart Created Date: 2/2/2003 6:21:58 PM Document presentation format: On-screen Show
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bioinformatique sont l'identification des g nes et la pr diction de leur ... Toutes les applications de l'informatique la biologie. - tude in silico de la ...
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Phenetic versus ... like network expressing phenetic relationships is called a ... approach, whereas the UPGMA method is a typical phenetic method. ...
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Lecture 4. Information Distance (Textbook, Section 8.3, and Li et al: Bioinformatics, 17:2(2001), 149-154, Li et al, SODA2003) In classical Newton world, we use ...
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What comes from Biology (genetics) and what comes from cultural development? ... Metaphoric transfer - joking and cursing. Ability to change roles in a dialogue ...
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salamander. frog. 0. 0. Distance Based Methods. Iterative ... In our case, one pair has zero distance: Mr. salamander & Mr. frog. Algorithm - 1st Iteration: ...
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The most important are the chloroplasts. ... Polyphyletic (Reptiles) NODE. BRANCH. Phylogeny Estimation. Branch-and-Bound. Least Squares ...
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Parsimony - Maximum likelihood - Bayesian likelihood ... Parsimony on cleaned alignment, with ML branches; rooted(?) ...what about branch lengths? ...
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gene segments and the whole mitochondrial genome. Fig. 25 Estimating the sample error ... Restriction site analysis and RFLP of coding and non-coding nuclear DNA ...
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Phenetic approach: Trees are based on some measure of distance between the leaves ... either cladistic (e.g. gene order) or phenetic ...
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Phylogenetic Analysis Introduction to bioinformatics Stinus Lindgreen stinus@binf.ku.dk Bioinformatics Centre, University of Copenhagen Outline of the lecture What is ...
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LS. ME. NJ. Distance calculation (which model?) Model? MP. Wheighting? ... Construction of phylogenetic trees. Science 155, 279-284. Phylogenies from proteins ...
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the more you know about the compared proteins and the method used, ... Methods in Enzymology 224, 456-487. 1. 2. 3. 4. 5. Align Sequences. Phylogenetic signal? ...
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The Molecular Clock ... molecular clocks more reasonable. Relative Rate Test. Test whether sets of sequences are evolving at equal rates (local molecular clock ...
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CH. 17 HISTORY OF LIFE Water carries small rock particles to lakes and seas. Dead organisms are buried by layers of sediment, which forms new rock.
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... Kirsty Bates, Margaret Biswas, Marie-Claude Blatter Garin, Brigitte ... secretarial assistance: Veronique Mangold, Claudia Sapsezian, Margaret Shore-Nye, ...
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Maximum-Parsimony. Maximum-Likelihood. tree cost. 18. Previous Approaches ... Parsimony, Least-Squares. Prefer distant trees. 32. Future Work. Generalize GNJ ...
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1950 Complementary Bases discovered. Edwin Chargaff. 1953 DNA is a ... Determine expression mechanisms via identifying alternative splicing regions. Proteomics ...
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Chaining Chain Letters. Charles H. Bennett collected 33 copies 1980--1997. ... with love all things are possible. this paper has been sent to you for good luck. ...
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Andrea G. B. Tettamanzi Scopi Data una famiglia di sequenze, trovare l albero di mutazione pi parsimonioso ricostruire l albero filogenetico valutare la ...
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and Functional Genomics by Jonathan Pevsner Charles Darwin's theory of evolution. ... Was Darwin correct that humans are closest. to chimps and gorillas? ...
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Algorithms versus ... with the best value for the objective function (may use algorithms) ... In criterion-based methods, algorithms are merely tools used ...
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Identifying unambiguously homologous positions is ... Barton-Stenberg multiple alignment ... Iterative refinement methods: Barton-Stenberg multiple alignment ...
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The Jukes-Cantor model states that all states {A,C,G,T} and all ... Under the Jukes-Cantor model where all point mutations are equally likely the correction is: ...
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PHYLIP package contains Fitch algorithm. Triangle method ... Fitch. Continue in this fashion, add each species to all possible places. ...
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Edges can be directed, then (vi,vj) is viewed as different ... Example: Human, Chimp, Gorilla & Orangutan with root. position 1 2 3 4 5 6 7 8 9 12.586 ...
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Define a node k with daughter nodes i and j, and place it at. height di,j/2. ... dAC dBD= dAD dBC= a b c d 2x = dAB dCD 2x. The 4-point condition ...
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Molecular Evolution: Plan for week Monday 3.11: Basics of Molecular Evolution Lecture 1: 9-10.30 Molecular Basis and Models I (JH) Computer : 11-12.30 PAUP ...
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and we want to know how similar they are. What is the basis for their ... Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. ...
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For unrooted trees with k leaves and internal nodes with 3 incoming edges, the following holds: ... Ultra Metric (distance function originates from tree) ...
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Analyses can be pursued with decreasing certainty towards the Twilight Zone ... around this threshold is the Twilight Zone, where alignments may appear ...
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Department of Zoology, The Natural History Museum, London. Inferring ... Aliphatic. Tiny. Aromatic. Charged. Taylor's Venn diagram of amino acids properties. K ...
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Linnaeus (18th Century): familiar hierarchical classification scheme of life: ... chimp mtDNA (Ingman et al, 2000), and primate retroviruses (Salemi et al., 2000) ...
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V4 Prediction of Phylogenies based on single genes. Material of this lecture taken from ... Suppose that we know that the great apes are a monophyletic group. ...
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AN INTRODUCTION TO AMINO ACID EXCHANGE MATRICES Robert Hirt Institute for Cell and Molecular Biosciences, Newcastle University, UK ...
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