LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters

By M. Kuhner. Bioinform., 2006

658 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/02e66dd4e54a0d1d91af97b931fb44910a18adb6

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Citations in the corpus

Phylogeny and comparative phylogeography of Sclerurus (Aves: Furnariidae) reveal constant and cryptic diversification in an old radiation of rain forest understorey specialists (2013, methodology): “…genetic summary statistics and estimated parameters such as genetic diversity (Q) and population growth rate (g) using the lamarc package (Kuhner, 2006). lamarc implements a MCMC method for sampling genealogies and calculates a likelihood curve used to determine the values of Q and g…”
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING? (2009, methodology): “Some recent phylogeographic approaches that incorporate recombination within loci into the model for multlocus data appear promising (Kuhner 2006; Becquet and Przeworski 2007).”
Distribution modelling and statistical phylogeography: an integrative framework for generating and testing alternative biogeographical hypotheses (2007, methodology): “The parameter h might be estimated using a coalescent-based program (e.g. using lamarc: Kuhner, 2006), as might an estimate of a population growth parameter in the event that a constant effective population size is not a reasonable assumption.”
Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 (2018, methodology): “2014), LAMARC (Kuhner 2006), Migrate (Beerli 2006), MrBayes (Ronquist et al.”
Integrating ensemble species distribution modelling and statistical phylogeography to inform projections of climate change impacts on species distributions (2013, methodology): “6 (Kuhner 2006).”
Non-linear regression models for Approximate Bayesian Computation (2008, methodology): “Although many likelihood-based methods have been proposed in this framework, these meth-ods are restricted to particular demographic and genetic processes (Stephens and Donnelly 2000; Wilson et al. 2003; Kuhner 2006; Hey and Nielsen 2007).”
Genome-Wide Inference of Ancestral Recombination Graphs (2013, background): “During the past two decades, various attempts have been made to perform explicit inference of ARGs using techniques such as importance sampling [19,22] (see also [23]) and Markov chain Monte Carlo sampling [24–27].”
How to use MIGRATE or why are Markov chain Monte Carlo programs difficult to use (2009, methodology): “Recently, the programs MIGRATE (Beerli 2006) and LAMARC (Kuhner 2006) were improved and can run both BI and ML.”
Unified Framework to Evaluate Panmixia and Migration Direction Among Multiple Sampling Locations (2010, background): “…of the original n-coalescent of Kingman to multiple populations with migration (Strobeck 1987; Hudson 1991) leads to probabilistic inference programs that consider potentially complex migration patterns among sampling locations (for example, Beerli and Felsenstein 2001; Beerli 2006; Kuhner 2006).”