ArticleBMC bioinformatics2015
Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Learning genotype-phenotype associations from gaps in multi-species sequence alignments.Briefings in bioinformatics · 2024Article
- The Promise of Inferring the Past Using the Ancestral Recombination Graph.Genome biology and evolution · 2024Article
- Likelihood-Based Tests of Species Tree Hypotheses.Molecular biology and evolution · 2023Article
- Efficient ancestry and mutation simulation with msprime 1.0.Genetics · 2022Article
- Article
- Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species.Proceedings. Biological sciences · 2020Article
- PRANC: ML species tree estimation from the ranked gene trees under coalescence.Bioinformatics (Oxford, England) · 2020Article
- Chimerism and population dieback alter genetic inference related to invasion pathways and connectivity of biofouling populations on artificial substrata.Ecology and evolution · 2019Article
- NANUQ: a method for inferring species networks from gene trees under the coalescent model.Algorithms for molecular biology : AMB · 2019Article
- Modeling Hybridization Under the Network Multispecies Coalescent.Systematic biology · 2018Article
- Incomplete lineage sorting impacts the inference of macroevolutionary regimes from molecular phylogenies when concatenation is employed: An analysis based on Cetacea.Ecology and evolution · 2018Article
- Inferring rooted species trees from unrooted gene trees using approximate Bayesian computation.Molecular phylogenetics and evolution · 2017Article
- Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent.Systematic biology · 2017Article
- On the importance of skewed offspring distributions and background selection in virus population genetics.Heredity · 2016Review
- Does Gene Tree Discordance Explain the Mismatch between Macroevolutionary Models and Empirical Patterns of Tree Shape and Branching Times?Systematic biology · 2016Article
- Coalescent inferences in conservation genetics: should the exception become the rule?Biology letters · 2016Review
- Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes.PLoS computational biology · 2016Article
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4 authors.
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Abstract
backgroundThere has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously.
resultsHybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman's coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes.
conclusionsHybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.
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