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No Slide Title
No Slide Title

... • To introduce the theory and practice of phylogenetic inference from molecular data ...
Evolution/Phylogeny
Evolution/Phylogeny

... 1. Make star tree with ‘fake’ distances (we need these to be able to calculate total branch length) 2. Check all n(n-1)/2 possible pairs and join the pair that leads to smallest total branch length. You do this for each pair by calculating the real branch lengths from the pair to the common ancestor ...
From phylogenetic trees to networks
From phylogenetic trees to networks

... evolutionary history of genes, populations, species. They are typically reconstructed with a wide range of algorithms from the comparison of very long strings representing the molecular (DNA or protein) sequences found across different organisms. Phylogenetic reconstruction is part of the daily rout ...
L1KProcs: an R package for L1000 data processing and analysis
L1KProcs: an R package for L1000 data processing and analysis

... • L1KProcs is an R package and interface for LINCS L1000 data preprocessing and compound signature detection in both textmode and graphic-mode way. • Additionally, it is a library for existing L1000 processed expression data and their connections (EGEM library). ...
Document
Document

... • The 3/4 and 4/3 terms reflect that there are four types of nucleotides and three ways in which a second nucleotide may not match a first - with all types of change being equally likely (i.e. unrelated sequences should be 25% identical by chance alone) ...
A Platform for Cluster Analysis of Next
A Platform for Cluster Analysis of Next

... The purpose of gene expression data clustering analysis is clustered genes with the same or similar functions to help explore the gene function and regulatory network. The past is mainly based on microarray gene expression data, in recent years due to the development of next-generation sequencing te ...
A Bayesian Method for Rank Agreggation
A Bayesian Method for Rank Agreggation

... The method is usually applied to rank the top K candidates, so P is KK matrix ◦ Let U be the list of genes that hare ranked as top K at least once in some experiment ◦ For each pair of genes in U, let mi , j  1 if for a majority of experiments i is ranked above j. ◦ Define Pi , j  mi , j / | U |, ...
S6. Phylogenetic results: complementary analyses Bayesian
S6. Phylogenetic results: complementary analyses Bayesian

... S6. Phylogenetic results: complementary analyses Bayesian Inference analyses with MrBayes 1.2, with characteristics as described above for the main analyses, were also carried out under different partition schemes to understand whether these would influence the general topology of the Madascincus ph ...
Trees
Trees

... Amino-acid sites are partially ordered characters. An amino acid cannot change into all other amino acids in a singe step, as sometimes 2 or 3 steps are required. For example, a tyrosine may only change into a leucine through an intermediate state, i.e., phenylalanine or histidine. ...
Algorithms and Data Analysis in Microarray Technology
Algorithms and Data Analysis in Microarray Technology

... Why Normalize Data ...
File
File

... The main idea of decision tree construction tree is to evaluate different attributes and different partitioning conditions, and pick the attributes and partitioning condition that results in the maximum information gain ratio. The same procedure works recursively on each of the sets resulting from t ...
Hierarchical Clustering in R
Hierarchical Clustering in R

... • How to find out what packages are actually installed locally – (.packages()) ...
KS3 curriculum links (England)
KS3 curriculum links (England)

... heredity as the process by which genetic information is transmitted from one generation to the next a simple model of chromosomes, genes and DNA in heredity, including the part played by Watson, Crick, Wilkins and Franklin in the development of the DNA model differences between species the variation ...
Exploratory Data Analysis Tools for Phylogenetics: Visualizing
Exploratory Data Analysis Tools for Phylogenetics: Visualizing

... and some misleading (e.g. long branch attraction, compositional bias, changing patterns of variable sites). ...
Slajd 1
Slajd 1

... The construction of phylogenetic trees from numerical methods The principle of maximum parsimony (Occam’s razor) holds that we should accept that phylogenetic tree that can be constructed with the least number of morphological changes. The raw data Species A B C D E ...
tree - Tecfa
tree - Tecfa

... Maximizes the likelihood of observing the sequence data for a specific model of character state changes Likelihood of a site = Sum of probabilities of every possible reconstruction of ancestral states at the internal nodes Likelyhood of the tree = Product of the likelihoods for all sites (=sum of lo ...
Objective 2.0
Objective 2.0

... markers). By adding genetic markers to their tool-chest, breeders will be able to select superior trees more accurately, more rapidly, and at lower cost than using traditional approaches alone. These enhanced approaches will permit greater utilization of the abundant genetic variation inherent in tr ...
Global Similarity Between Multiple Bionetworks
Global Similarity Between Multiple Bionetworks

...  Sequence sorting: The nodes are generally weighted by different attributes; however, the occurrence of same nodes in graphs greatly increase the complexity for finding the maximal global similarities between two networks.  Transitivity: Especially in functional networks, the transitivity should b ...
Networks: expanding evolutionary thinking
Networks: expanding evolutionary thinking

... data carry the promise of fascinating insights into treelike processes, non-treelike processes are commonly observed. Network analysis is a readily available and ideal tool that reduces the danger of misinterpreting such data. Tackling error with networks There are long-standing controversies regard ...
Dry Lab – More Tree Analayses
Dry Lab – More Tree Analayses

... Question 3. Which clades have high support? Are there any inconsistencies relative the “true tree” that have good support? ...
View the seminar poster
View the seminar poster

... totalling   more   than   700   species   worldwide.   Subjected   to   phylogene5c   analysis   since   the   late  1990s,  early  studies  drew  on  small  sets  of  external  morphological  characters,  mostly   those  used  in  classical ...
Bioinformatics and Supercomputing
Bioinformatics and Supercomputing

... action of the Alu ‘restriction’ endonucleous. •Discovery of Alu subfamillies led to hypothesis of master/ source genes. AGCT •Reveal ancestry because individuals only share particular sequence insertion if the share an ancestor. •Can identify similarities of functional, structural, or evolutionary r ...
Document
Document

...  ClustalW and Phylip do bootstrap operations automatically  Bootstrapping involves these steps: ...
Phylogeny
Phylogeny

... confidence (e.g. bootstrap values) - sadly we only rarely see these… ...
Intraspecific gene genealogies: trees grafting into networks
Intraspecific gene genealogies: trees grafting into networks

... network is built by taking these splits and combining them successively when splits are incompatible, a loop is introduced to indicate that there are alternative splits fast, nucleotide or protein data, allows for the inclusion of models of nucleotide substitution or amino acid replacement, bootstra ...
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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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