96 Result(s)
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English
Bioinformatics
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Exploring Population Structure with Admixture Models and Principal Component Analysis
Population structure is a commonplace feature of genetic variation data, and it has importance in numerous application areas, including evolutionary genetics, conservation genetics, and human genetics. Underst...
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Avian Population Genomics Taking Off: Latest Findings and Future Prospects
Birds are one of the most recognizable and diverse groups of organisms on earth. This group has played an important role in many fields, including the development of methods in behavioral ecology and evolution...
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Ancestral Population Genomics with Jocx, a Coalescent Hidden Markov Model
Coalescence theory lets us probe the past demographics of present-day genetic samples and much information about the past can be gleaned from variation in rates of coalescence event as we trace genetic lineage...
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Inference of Ancestral Recombination Graphs Using ARGweaver
This chapter describes the usage of the program ARGweaver, which estimates the ancestral recombination graph for as many as about 100 genome sequences. The ancestral recombination graph is a detailed descripti...
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A Population Genomics Lexicon
Population genomics is a growing field stemming from soon a 100 years of developments in population genetics. Here, we summarize the main concepts and terminology underlying both theoretical and empirical stat...
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Genomics of Long- and Short-Term Adaptation in Maize and Teosintes
Maize is an excellent model for the study of plant adaptation. Indeed, post domestication maize quickly adapted to a host of new environments across the globe. And work over the last decade has begun to highli...
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Data Management and Summary Statistics with PLINK
PLINK is a versatile program which supports data management, quality control, and common statistical computations on matrices of genomic variant calls, in a computationally efficient manner. In population geno...
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Population Genomics of Fungal Plant Pathogens and the Analyses of Rapidly Evolving Genome Compartments
Genome sequencing of fungal pathogens have documented extensive variation in genome structure and composition between species and in many cases between individuals of the same species. This type of genomic var...
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Detecting Positive Selection in Populations Using Genetic Data
High-throughput genomic sequencing allows to disentangle the evolutionary forces acting in populations. Among evolutionary forces, positive selection has received a lot of attention because it is related to th...
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Genomic Access to the Diversity of Fishes
The number of fishes exceeds that of all other vertebrates both in terms of species numbers and in their morphological and phylogenetic diversity. They are an ecologically and economically important group and ...
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MSMC and MSMC2: The Multiple Sequentially Markovian Coalescent
The Multiple Sequentially Markovian Coalescent (MSMC) is a population genetic method and software for inferring demographic history and population structure through time from genome sequences. Here we describe...
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Population Genomics of the House Mouse and the Brown Rat
Mice (Mus musculus) and rats (Rattus norvegicus) have long served as model systems for biomedical research. However, they are also excellent models for studying the evolution of populations, subspecies, and speci...
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Coalescent Simulation with msprime
Coalescent simulation is a fundamental tool in modern population genetics. The msprime library provides unprecedented scalability in terms of both the simulations that can be performed and the efficiency with whi...
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Population Genomics of Transitions to Selfing in Brassicaceae Model Systems
Many plants harbor complex mechanisms that promote outcrossing and efficient pollen transfer. These include floral adaptations as well as genetic mechanisms, such as molecular self-incompatibility (SI) systems...
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Processing and Analyzing Multiple Genomes Alignments with MafFilter
As the number of available genome sequences from both closely related species and individuals within species increased, theoretical and methodological convergences between the fields of phylogenomics and popul...
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Neurospora from Natural Populations: Population Genomics Insights into the Life History of a Model Microbial Eukaryote
The ascomycete filamentous fungus Neurospora crassa played a historic role in experimental biology and became a model system for genetic research. Stimulated by a systematic effort to collect wild strains initiat...
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Population Genomics on the Fly: Recent Advances in Drosophila
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted ...
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A Computational Vaccine Designing Approach for MERS-CoV Infections
The aim of this study was to use IEDB software to predict the suitable MERS-CoV epitope vaccine against the most known world population alleles through four selecting proteins such as S glycoprotein and envelo...
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polyDFE: Inferring the Distribution of Fitness Effects and Properties of Beneficial Mutations from Polymorphism Data
The possible evolutionary trajectories a population can follow is determined by the fitness effects of new mutations. Their relative frequencies are best specified through a distribution of fitness effects (DF...
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Correction to: Choosing the Best Gene Predictions with GeneValidator
This book was published with References 17 and 18 in the incorrect order.
