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MultipleSequenceAlignment
MultipleSequenceAlignment

... phylogenetic tree, aligns the most-alike pair, and incrementally adds sequences to the alignment in order of “alikeness” as indicated by the tree.) Differs from dynamic programming method for MSA in that it doesn’t refine the “first-cut” MSA by doing a full search through the reduced search space. ( ...
Species tree
Species tree

... • Bininda-Emonds ORP (2005). Supertree Construction in the Genomic Age. Methods in Enzymology 395: p.745-757. • Bininda-Emonds,OPRP, John L. Gittleman, Mike A. Steel (2002) The (super)Tree Of Life: Procedures, Problems, and Prospects. Annual Review of Ecology and Systematics, Vol. 33: 265-289. • Dag ...
Use DNA Sequencing to Trace the Blue Whale`s Evolutionary Tree
Use DNA Sequencing to Trace the Blue Whale`s Evolutionary Tree

... Although this is a genomics project, it is also about whales. To build the tree of the whale family, you will need to spend some time getting familiar with the scientific names and key features of about 25 whale and dolphin species. You will also learn about the blue whale's closest relatives that d ...
Ribosomal RNA Secondary Structure
Ribosomal RNA Secondary Structure

C tudi - DNA to Darwin
C tudi - DNA to Darwin

... a. Variations in the rate of evolution may lead to organisms being placed in the wrong place on an evolutionary tree (they may look very different when they are in fact closely-related). b. Any examples of convergent evolution could be suggested here, for example, wings in bats and birds, camera- ...
Matlab Bioinfo Toolbox QuickGuide
Matlab Bioinfo Toolbox QuickGuide

... to genomic and proteomic data formats, analysis techniques, and specialized visualizations for genomic and proteomic sequence and microarray analysis. The key features of the basic categories in the Bioinformatics Toolbox will be presented in the following sections. This guide does not replace the e ...
Chapter 25 Presentation
Chapter 25 Presentation

... For example, let’s look at hinged jaws. These are absent in lampreys, but are found in other members of the ingroup-this represents a branch point. The cladogram we’ve developed isn’t a phylogenetic tree, we need more information from fossils, etc. to indicate when the groups first appeared. ...
Phylogenetic Place of Guinea Pigs: No Support of the Rodent
Phylogenetic Place of Guinea Pigs: No Support of the Rodent

... Graur et al’s ( 199 1) hypothesis that the guinea pig-like rodents have an evolutionary origin within mammals that is separate from that of other rodents (the rodent-polyphyly hypothesis) was reexamined by the maximum-likelihood method for protein phylogeny, as well as by the maximum-parsimony and n ...
1) of
1) of

... Often, data FAIL both tests - there are conflicts, and distances from sister species to the outgroup are not the same - revealing that evolution was not exclusively divergent and did not proceed at an exactly constant rate. What to do? More sophisticated approaches can be used. Maximal likelihood - ...
Presentation Tuesday
Presentation Tuesday

... similarity. Fast, but not a direct reconstruction of “what happened in evolution”. Neighbor Joining is the often used method here ...
Hemiplasy: A New Term in the Lexicon of Phylogenetics
Hemiplasy: A New Term in the Lexicon of Phylogenetics

... that can lead to genuine discordances between particular gene trees (components of the genome) and a composite or overall species phylogeny. We suggest the word hemiplasy, because the responsible lineage sorting processes have homoplasy-like consequences despite the fact that the character states th ...
Appendix S2.
Appendix S2.

... Most published trees contained only a few taxa of interest for any particular group. Therefore, we were often forced to use multiple trees which may have employed different characters and methods in their analyses to place particular taxa into our tree (e.g. Elapideae, see below). ...
A DNA-sequence based phylogeny for triculine snails (Gastropoda
A DNA-sequence based phylogeny for triculine snails (Gastropoda

... together with considerable bias among the 6 different types of nucleotide substitution (see Results). In such cases the ML method, making possible a fully optimized model of substitution, is considered more robust than other phylogenetic methods (Nei, 1991). A Bayesian method was also used because t ...
TreeFitter commands
TreeFitter commands

... Tree fitting has important applications in historical biogeography, coevolution and gene tree-species tree fitting [see recent reviews by \Page, 1998 #1419; Ronquist, 1998 #760]. A general characteristic of these problems is that two different kinds of trees are fitted to each other because we are i ...
Comp. Genomics
Comp. Genomics

... • Viterbi, forward-backward etc. – as usual ...
Molecular phylogeny, part B
Molecular phylogeny, part B

... Multigene family: A group of genes, clustered or dispersed, with related nucleotide sequences. Multiple alignment: An alignment of three or more nucleotide sequences. Multiple hit or multiple substitution: The situation that occurs when a single nucleotide in a DNA sequence undergoes two mutational ...
Classification and Phylogeny
Classification and Phylogeny

... The ancestral state of character j is present in species 2. This is an evolutionary reversal. ...
PowerPoint
PowerPoint

... 2. Parsimony – fewest number of evolutionary events (mutations) – relatively often fails to reconstruct correct phylogeny, but methods have improved recently 3. Maximum likelihood – L = Pr[Data|Tree] – most flexible class of methods - user-specified evolutionary methods can be used ...
Concepts of Biology - Amazon Simple Storage Service (S3)
Concepts of Biology - Amazon Simple Storage Service (S3)

... other organisms not pictured, such as fungi and protists. At each sublevel, the organisms become more similar because they are more closely related. Before Darwin’s theory of evolution was developed, naturalists sometimes classified organisms using arbitrary similarities, but since the theory of evo ...
Amsterdam 2004 - Theoretical Biology & Bioinformatics
Amsterdam 2004 - Theoretical Biology & Bioinformatics

... multidomain proteins by examining the pictorial representation of the BLAST search outputs. The sequences of detected multidomain proteins are split into single-domain segments and steps 1–4 are repeated with these sequences, which results in the assignment of individual domains to COGs in accordanc ...
The Graph of Life
The Graph of Life

... •The three trees seem quite different: (((((((Scer,Spar),Smik),Skud),Sbay),Scas),Sklu),Calb) (((((((Scer,Spar),Smik),Skud),Sbay),Sklu),Scas),Calb) (((((Skud,Sbay),((Scer,Spar),Smik)),Scas),Sklu),Calb) In particular, Skud seems to move a lot. But our graph showed multiple ancestry for Scas only. ...
Unoshan_project
Unoshan_project

... but they are not in the usual Watson-Crick geometry. Sequences can diverge from a common ancestor because mutations occur. Those mutations can then be fixed into the evolving population. The Maximum Likelihood method is used for the analysis of DNA and amino acid sequence data in an attempt to answe ...
25_DetailLectOutjk_AR
25_DetailLectOutjk_AR

... In general, the more points of resemblance that two complex structures have, the less likely it is that they evolved independently.  For example, the skulls of a human and a chimpanzee are formed by the fusion of many bones.  The two skulls match almost perfectly, bone for bone.  It is highly unl ...
PowerPoint
PowerPoint

... Consider the codons specifying aspartic acid and lysine: both start AA, lysine ends A or G, and aspartic acid ends T or C. So, if the rate at which C changes to T is higher from the rate that C changes to G or A (as is often the case), then more of the changes at the third position will be synonymou ...
RidgeRace: ridge regression for continuous ancestral character
RidgeRace: ridge regression for continuous ancestral character

... and Contml (Felsenstein, 1993). One of the simplest ways to reconstruct a continuous ancestral character state was established with Felsenstein’s algorithm for ‘Phylogenetic Independent Contrasts’ (Felsenstein, 1985). In the Phylogenetic Independent Contrasts algorithm, ancestral values are computed ...
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Maximum parsimony (phylogenetics)

In phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes is to be preferred. Under the maximum-parsimony criterion, the optimal tree will minimize the amount of homoplasy (i.e., convergent evolution, parallel evolution, and evolutionary reversals). In other words, under this criterion, the shortest possible tree that explains the data is considered best. The principle is akin to Occam's razor, which states that—all else being equal—the simplest hypothesis that explains the data should be selected. Some of the basic ideas behind maximum parsimony were presented by James S. Farris in 1970 and Walter M. Fitch in 1971.Maximum parsimony is an intuitive and simple criterion, and it is popular for this reason. However, although it is easy to score a phylogenetic tree (by counting the number of character-state changes), there is no algorithm to quickly generate the most-parsimonious tree. Instead, the most-parsimonious tree must be found in ""tree space"" (i.e., amongst all possible trees). For a small number of taxa (i.e., less than nine) it is possible to do an exhaustive search, in which every possible tree is scored, and the best one is selected. For nine to twenty taxa, it will generally be preferable to use branch-and-bound, which is also guaranteed to return the best tree. For greater numbers of taxa, a heuristic search must be performed.Because the most-parsimonious tree is always the shortest possible tree, this means that—in comparison to the ""true"" tree that actually describes the evolutionary history of the organisms under study—the ""best"" tree according to the maximum-parsimony criterion will often underestimate the actual evolutionary change that has occurred. In addition, maximum parsimony is not statistically consistent. That is, it is not guaranteed to produce the true tree with high probability, given sufficient data. As demonstrated in 1978 by Joe Felsenstein, maximum parsimony can be inconsistent under certain conditions, such as long-branch attraction.
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