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Document
Document

...  The function of many, typically 50%, of translated proteins can be inferred from sequence comparison with previously characterized sequences  The assignment of function by homology gives only a partial understanding of a protein’s role within a cell  A more complete understanding of a protein fu ...
Tree Thinking Assessment Quiz
Tree Thinking Assessment Quiz

... on the left, and the gray branches indicate uncertainty in character reconstruction. What does a comparison of these two figures tell us about the evolution of plant secondary chemistry? a. The four groups of chemically similar species each constitutes a distinct evolutionary lineage b. The group co ...
biol2007 - evolutionary trees and their uses
biol2007 - evolutionary trees and their uses

... Parsimony methods have been criticised for failing to use all of the information available – often only small proportions of datasets are used. Some researchers seek to exploit information more efficiently and (often using sophisticated statistical tests) seek to choose best tree among all possible ...
Phylogenetic analysis
Phylogenetic analysis

... molecular sequences: reconstruct the evolutionary history of the species involved. A gene phylogeny only describes the evolution of that particular gene or encoded protein. This sequence may evolve more or less rapidly than other genes in the genome. The evolution of a particular sequence does not n ...
Removing Unwanted Variation from High-Throughput Omic Data
Removing Unwanted Variation from High-Throughput Omic Data

... have been carried out, with the hope of understanding, predicting or discovering factors of interest such as prognosis or the subtypes of a cancer. The same applies to proteomic and metabolomic data, and to several other kinds of data. Large studies are often carried out over several years, and invo ...
NETWORK ANALYSIS COURSE
NETWORK ANALYSIS COURSE

... Advanced topics in trait mapping, estimates of precision, estimates of power Exercise: Empirical precision of monogenic QTLs 2a. Network analysis seeded by single genes, transcripts, proteins... Review of mouse, rat, and human data sets Exercise: Cdc20 and the cell cycle Correlation to PC eigentrait ...
ODD-Genes - National e
ODD-Genes - National e

... Researcher can reproduce this initial condition for repeated analyses Researcher need not perform each step manually and serially, or ask dedicated statistician to do so. ...
Molecular evolution and phylogenetic implications in clinical research
Molecular evolution and phylogenetic implications in clinical research

... to making errors during DNA replication, which means that duplicates are not always identical to the original. If DNA replication is accurate, there would be no variation on which natural selection could act. Errors are thus the key to evolution. In many cases, the classification of the species was ...
here - CMBI
here - CMBI

... sequence changes to other character states • BLOck SUbstitution Matrix (BLOSUM) is based on observed substitutions between proteins with e.g. >62% sequence identity ...
Molecular Phylogeny
Molecular Phylogeny

... • A phylogenetic tree is characterised by its topology (form) and its length (sum of its branch lengths) ; • Each node of a tree is an estimation of the ancestor of the elements included in this node; • There are 3 main classes of phylogenetic methods for constructing phylogenies from sequence data ...
Glycemia and Wt Mngt. Olz
Glycemia and Wt Mngt. Olz

... there is less than a 5% chance of obtaining a difference this large or larger. c) There is a 95% chance that if the study is repeated, the result will be replicated. d) There is a 95% chance that there is a real difference between the two population means. Adapted from: Wulff HR, Andersen B, Branden ...
introduction to molecular phylogeny
introduction to molecular phylogeny

... tree (that whose total branch length is minimum). In that sense, the NJ method is very similar to parsimony because branch lengths represent substitutions. NJ produces always unrooted trees, that need to be rooted by the outgroup method. NJ always finds the correct tree if distances are tree-like. N ...
lecture 03 - phylogenetics - Cal State LA
lecture 03 - phylogenetics - Cal State LA

... Since we can’t travel back in time to identify common ancestors, relationships of existing species must be estimated or inferred from data – therefore, a phylogeny is always a hypothesis ...
RidgeRace: ridge regression for continuous ancestral character
RidgeRace: ridge regression for continuous ancestral character

... Such reconstructions can reach into the distant past and can provide insights into the history of a population or a set of species when fossil data are not available, or they can be used to test evolutionary hypotheses, e.g. on the co-evolution of traits. Typical methods for ancestral character stat ...
A common ancestor
A common ancestor

... Pairwise Sequence Alignment • Methods – Global alignment • Closely related sequences • Similar length ...
reduce
reduce

... • reduces experimental noise and is well suited for uncovering groups of genes • a quantitative expression of the widespread notion18 that transcription initiation occurs through the recruitment of the polymerase by reversible binding to transcription factors and hence to the regulatory sequences • ...
download PDF program in pamphlet form
download PDF program in pamphlet form

... Linguists have for a century suggested a common linguistic heritage for NaDene and Yeniseian, but only recently has a case been made using traditional methods of historical reconstruction (Vajda 2010). Our work responds to challenges to use alternative methodologies to evaluate this hypothesis (Camp ...
Lecture PPT - Carol Lee Lab
Lecture PPT - Carol Lee Lab

... • They can be DNA nucleotides or other heritable traits • They are used to group taxa that are more closely related to one another ...
pptx
pptx

... expression profile. ...
manual
manual

... -l LSCALE, --length scale=LSCALE Sequence lengths scaling for alignments. Each alignment in each simulation can be scaled with the same number. -v THETA, --theta=THETA θ parameter for generating gene trees from the species trees before generating alignments along the species tree. For the definition ...
2_Outline_BIO119_div..
2_Outline_BIO119_div..

... A. General features of a molecular marker? ...
Lecture PPT - Carol Lee Lab
Lecture PPT - Carol Lee Lab

... • They can be DNA nucleotides or other heritable traits • They are used to group taxa that are more closely related to one another ...
Practical theory (15-20 min) A phylogeny is the representation of the
Practical theory (15-20 min) A phylogeny is the representation of the

... Phylogram: tree that shows the relations and distances among sequences. The length of the branches are proportional to the distance between two sequences. ...
Lectures 21, 22, and 23: Phylogenic Trees and Evolution Steven
Lectures 21, 22, and 23: Phylogenic Trees and Evolution Steven

... Because the various algorithms and heuristics give different trees on the same data, more evidence is needed than a single tree to define the history. For this reason, there are suites of programs (e.g. Phylip) which contain implementations of many different tree construction algorithms and heuristi ...
Document
Document

... Likelihood • Calculate the Likelihood for each base position in the sequence and summarizes across all base positions. • The ML tree is the tree that produces the highest likelihood. • Evaluates the branching structure of the tree, and also the branch length, using similar tree-searching strategies ...
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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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