ArticleBMC genetics2012
EggLib: processing, analysis and simulation tools for population genetics and genomics.
Article in BMC genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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66 citing papers in PubMed.
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- A brief history and popularity of methods and tools used to estimate micro-evolutionary forces.Ecology and evolution · 2021Review
- Selection and isolation define a heterogeneous divergence landscape between hybridizing Heliconius butterflies.Evolution; international journal of organic evolution · 2021Article
- Genetic diversity and population structure of the amylolytic yeast Saccharomycopsis fibuligera associated with Baijiu fermentation in China.Journal of microbiology (Seoul, Korea) · 2021Article
- Improved redox homeostasis owing to the up-regulation of one-carbon metabolism and related pathways is crucial for yeast heterosis at high temperature.Genome research · 2021Article
- Adaptive introgression from maize has facilitated the establishment of teosinte as a noxious weed in Europe.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation.PLoS biology · 2020Article
- Lateral Gene Transfer Shapes Diversity ofFrontiers in cellular and infection microbiology · 2020Article
- Programmed Cell Death inGenetics · 2019Article
- Local adaptation drives the diversification of effectors in the fungal wheat pathogen Parastagonospora nodorum in the United States.PLoS genetics · 2019Article
- Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia.Molecular ecology · 2019Article
- Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity.Current biology : CB · 2019Article
6 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
backgroundWith the considerable growth of available nucleotide sequence data over the last decade, integrated and flexible analytical tools have become a necessity. In particular, in the field of population genetics, there is a strong need for automated and reliable procedures to conduct repeatable and rapid polymorphism analyses, coalescent simulations, data manipulation and estimation of demographic parameters under a variety of scenarios.
resultsIn this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C++/Python software package providing efficient and easy to use computational tools for sequence data management and extensive population genetic analyses on nucleotide sequence data. EggLib is a multifaceted project involving several integrated modules: an underlying computationally efficient C++ library (which can be used independently in pure C++ applications); two C++ programs; a Python package providing, among other features, a high level Python interface to the C++ library; and the egglib script which provides direct access to pre-programmed Python applications.
conclusionsEggLib has been designed aiming to be both efficient and easy to use. A wide array of methods are implemented, including file format conversion, sequence alignment edition, coalescent simulations, neutrality tests and estimation of demographic parameters by Approximate Bayesian Computation (ABC). Classes implementing different demographic scenarios for ABC analyses can easily be developed by the user and included to the package. EggLib source code is distributed freely under the GNU General Public License (GPL) from its website http://egglib.sourceforge.net/ where a full documentation and a manual can also be found and downloaded.
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