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Phylogenetic Analysis
Phylogenetic Analysis

... Tree-structure diagram showing the inferred evolutionary relationships between a set of objects ...
Schedule for workshop
Schedule for workshop

... (Vajda 2010). Our work responds to challenges to use alternative methodologies to evaluate this hypothesis (Campbell 2011, Diamond 2011) and contributes to a growing body of literature using bioinformatic methods to push the time depths at which linguistic comparison can test hypotheses of prehistor ...
Data Integration
Data Integration

... (e.g., ranks, correlation matrices), kernel-based analysis ...
Content Analysis: Overview of Concepts and Applications
Content Analysis: Overview of Concepts and Applications

... What is history? “These so-called facts which are the the same for all historians, commonly belong to the category of raw materials of the historian rather than of history itself … The necessity to establish these basic facts rests not with any quality in the facts themselves, but on an ‘a priori’ ...
RNASeqGUI
RNASeqGUI

... manner is of fundamental importance, although often neglected in many research paper. The need for RR increases dramatically as data analyses become more complex, involves larger datasets and more sophisticated computations, such as in the case of RNA-seq data analysis GUIs do not easily facilitate ...
CIT_b
CIT_b

... • A new hierarchical genotype representation: natural hierarchy in forming the solution and more protective genetic operation for functional components • Dynamic substructure library: defining and reusing selfemergent substructures in the evolutionary process. ...
Presentation
Presentation

... of biomedicine and pure biology research. GOALS: • Study the genetic causes of facial variation and facial abnormalities. • Study the evolutionary processes involved in craniofacial development. • Develop awareness, prevention and treatments for common genetic syndromes involving the face, such as c ...
Finding Sparse Gene Networks
Finding Sparse Gene Networks

... this difficulty as follows. We diagnose the matrix as multicollinear when a variance inflation factor (VIF) [1] is larger than a cutoff value, usually 10.0. We define the i-th VIF of a correlation coefficient matrix R by VIFi = rii , where rii is the i-th diagonal element of the inverse matrix of R. VIF ex ...
Two-point Linkage Analysis: a brief outline of theory
Two-point Linkage Analysis: a brief outline of theory

... families. The aim is to test whether the genetic linkage between a disease and its marker(s) is the same in all sub-groups. These groups are formed ad hoc on the basis of clinical or geographical criteria etc....  Let us assume that the total sample of families has been divided into n sub-groups (i ...
Stefan Zimmermann1,C. Seyboldt 2, F. Günther1, J
Stefan Zimmermann1,C. Seyboldt 2, F. Günther1, J

... within one month. The number of CDI in the hospital was much higher than the average of the previous month suggesting a C. difficile outbreak. Capillary gel electrophoresis-based PCR ribotyping was performed and resulting peak patterns were assigned to PCR ribotypes using the Webribo database. The r ...
Lecture 7-POSTED-BISC441-2012
Lecture 7-POSTED-BISC441-2012

... Taxon B (eg HUMANS!) C is more similar in sequence to A (d = 3) than to B (d = 7), but C and B are most closely related (that is, C and B shared a common ancestor more recently than either did with A). ...
How to find genes whose expression profile is similar
How to find genes whose expression profile is similar

... In some cases you have certain genes of interest and you would like to find other genes that are close to the genes of interest. This can be done using the genefinder function. You need to specify either the index position of the genes you want (which row of the expression array the gene is in) or t ...
EVALUATION OF INVESTIGATOR® STR GO! LYSIS BUFFER FOR
EVALUATION OF INVESTIGATOR® STR GO! LYSIS BUFFER FOR

... with great inter-locus and intra-color balance. Peak height balances were greater than 70% and there were few occurrences of off-scale data. The data quality of this method was comparable to the method currently used at the USACIL DNA Database; however, with the Investigator® STR GO! Lysis Buffer me ...
Statistical Data Analysis
Statistical Data Analysis

... statistically significant discriminator proteins as well as the biologic status. The selection of important proteins was based on Kruskal-Wallis test, Fisher’s exact test (dichotomize the expression level as present or not), t-test, Significance Analysis of Microarrays (SAM)5, Weighted Gene Analysis ...
Molecular Phylogenetic Analysis: Design and Implementation of
Molecular Phylogenetic Analysis: Design and Implementation of

... difference in lengths can appear due to sequencing errors (digitalizing the biological sample), mutations (insertions or deletions of one or more sites along the sequence) or because the researcher also wants to include fragments of the same genetic region that were used in other experiments. The se ...
Comparative Anatomy: Phylogenetics Assignment
Comparative Anatomy: Phylogenetics Assignment

... b. Which taxa are most closely related? Which taxa are the most distantly related? 5. Conduct a neighbor joining and maximum parsimony analysis on these data (do not bootstrap—I do not want your programs to crash). Print out these trees (consensus for the parsimony) to hand in and base the answers t ...
Maximum pseudo-likelihood estimation of species trees (MP
Maximum pseudo-likelihood estimation of species trees (MP

... The program is written in C. To compile the source code, type “make” (without quote) at the terminal window on Mac (or the Dos command window on PC). You need to set “architecture = ?” to the correct platform (mac, unix, or windows) in makefile. Currently, the parallel version is not available. Thus ...
Phylogeny slides
Phylogeny slides

... “Optimal” depends on multiple alignment scoring method No known (correct) efficient algorithms for this problem ...
such as for example in pairwise distance methods
such as for example in pairwise distance methods

... – they search for each column of the alignment, the simplest explanation for how the characters evolved. – For instance, MP involves a search for a tree with the fewest number of amino acid (or nucleotide character changes that account for the observed differences between the protein (gene) sequence ...
Artificial Intelligence Project #3 : Analysis of Decision Tree Learning
Artificial Intelligence Project #3 : Analysis of Decision Tree Learning

... Artificial Intelligence Project #3 : Analysis of Decision Tree Learning Using WEKA May 23, 2006 ...
Analysis of Crop Plant Genomes
Analysis of Crop Plant Genomes

... represented as a tree of evolution (often called a phylogenetic tree). ...
Language and genetics - Max-Planck
Language and genetics - Max-Planck

... Nevertheless, its discovery was the first small comparative historical linguistics, based pribreakthrough in understanding the genetic marily on similarities in vocabulary, can basis of human language4. make sense of language evolution over only the past few thousand years at most. The new project a ...
A1979HZ36300001
A1979HZ36300001

... Because of my interest in genetics, I was fascinated by the anomalies in the workshop data. Hoping naively that there might exist some 'hybrid' antigens (similar to those in rabbits) which are expressed only after appropriate alleles come together in an offspring, I came to Terasaki's laboratory to ...
Phylogenetics
Phylogenetics

... By adding one or several species you know are less related to any of the species you investigating then they are to one another, you get the time direction in the tree. So you have a rooted tree. 6. Build a tree using neighbor joining Name the output file from muscle 'infile' (if needed), then run ...
Phylogenetics Molecular Phylogenetics
Phylogenetics Molecular Phylogenetics

... a problem because of some change in behaviour? Or is there another explanation for their origin? Host species tree ...
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Quantitative comparative linguistics

Statistical methods have been used in comparative linguistics since at least the 1950s (see Swadesh list). Since about the year 2000, there has been a renewed interest in the topic, based on the application of methods of computational phylogenetics and cladistics to define an optimal tree (or network) to represent a hypothesis about the evolutionary ancestry and perhaps its language contacts. The probability of relatedness of languages can be quantified and sometimes the proto-languages can be approximately dated.The topic came the attention of the popular press in 2003 after the publication of a short study on Indo-European in Nature (Gray and Atkinson 2003). A volume of articles on Phylogenetic Methods and the Prehistory of Languages was published in 2006 as the result of a conference held in Cambridge in 2004.A goal of comparative historical linguistics is to identify instances of genetic relatedness amongst languages. The steps in quantitative analysis are (i) to devise a procedure based on theoretical grounds, on a particular model or on past experience, etc. (ii) to verify the procedure by applying it to some data where there exists a large body of linguistic opinion for comparison (this may lead to a revision of the procedure of stage (i) or at the extreme of its total abandonment) (iii) to apply the procedure to data where linguistic opinions have not yet been produced, have not yet been firmly established or perhaps are even in conflict.Applying phylogenetic methods to languages is a multi-stage process (a) the encoding stage - getting from real languages to some expression of the relationships between them in the form of numerical or state data, so that those data can then be used as input to phylogenetic methods (b) the representation stage - applying phylogenetic methods to extract from those numerical and/or state data a signal that is converted into some useful form of representation, usually two dimensional graphical ones such as trees or networks, which synthesise and ""collapse"" what are often highly complex multi dimensional relationships in the signal (c) the interpretation stage - assessing those tree and network representations to extract from them what they actually mean for real languages and their relationships through time.
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