PDF-Coalescent ModelsWith RecombinationBiostatistics 666Lecture 6 ...

Today. All these partitioned analyses of concatenated data sets make the assumption . t. hat all the genes share a common gene tree.. However there are several important reasons that phylogeny estimates from separate genes might be incongruent.. Category Intel models AMD modelswith UMAgraphics AMD modelswith discretegraphics Graphics Intel Graphics, IntelUMA (integrated) with shared videoUp to 251 MB on computers with1024 MB of system memoryU = amount of time there are k distinct lineages. Today Zhi. -Ming Ma. . ECM2013 . PolyU. . Email: mazm@amt.ac.cn . http://www.amt.ac.cn/member/mazhiming/index.html. A New Method for Coalescent Processes with Recombination . Summary of assumptions so far. We have covered the role of chance (parent choice), demography (population size) and mutation, in shaping genetic diversity. . Neutral Wright-Fisher . models. Parents are always chosen at random. This means no new mutations affect reproductive success of parents, i.e. . CSE280. Vineet Bafna. Expectation, and deviance. Statements such as the ones below can be made only if we have an underlying model that suggests what we should expect. . Recombination rates vary dramatically across the genome. CSE280. Vineet Bafna. Expectation, and deviance. Statements such as the ones below can be made only if we have an underlying model that suggests what we should expect. . Recombination rates vary dramatically across the genome. Genetics (SC1). Simon Myers . . Email: . myers@stats.ox.ac.uk. . Course webpage: . www.stats.ox.ac.uk/~myers/mathgen.html. Class problem sheets . are . posted . online (separate sheets for MSc and Part C). Gene Tree Probability. under the . Multispecies Coalescent . and its Application in the Inference of Population Tree. Yufeng. . Wu. Dept. of Computer Science & Engineering. University of Connecticut, USA. Tandy Warnow. Joint work with . Siavash. . Mirarab. , . Md. S. . Bayzid. , and others. Orangutan. Gorilla. Chimpanzee. Human. From the Tree of the Life Website. ,. . University . of . Arizona. Dates from Lock et al. Nature, 2011. Yufeng Wu. University of Connecticut. DIMACS Workshop on Algorithmics in Human Population-Genomics, 2009. 1. Coalescent Likelihood. D: . a set of binary sequences.. Coalescent genealogy: history with . to the Netflix Prize. by. Leenarat. . Leelapanyalert. Netflix Dataset. Over 100 million movie ratings with date-stamp (100,480,507 ratings). M = 17,770 movies. N = 480,189 customers. 1 (star) = no interest, 5(stars) = strong interest. population genetics I: models and drift. Reading. Course slides on the web. Hartl. and Clark, Principle of population genetics. Rick . Durret. – Probability models for DNA sequence evolution . Gillespie – Pop. Genetics, A concise guide.