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Efficient strategies for calculating blockwise likelihoods under the coalescent

https://doi.org/10.1101/016469
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The coalescent
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Estimation of the Spontaneous Mutation Rate in Heliconius melpomene
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Inferring population history from molecular phylogenies
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Approximating the coalescent with recombination
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Speciation in Heliconius Butterflies: Minimal Contact Followed by Millions of Generations of Hybridisation
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Genome-wide evidence for speciation with gene flow in Heliconius butterflies
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MULTILOCUS ANALYSES OF ADMIXTURE AND INTROGRESSION AMONG HYBRIDIZING HELICONIUS BUTTERFLIES
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A likelihood‐based comparison of population histories in a parasitoid guild
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TESTING THE CONSTANT-RATE NEUTRAL ALLELE MODEL WITH PROTEIN SEQUENCE DATA
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Estimation of the Branch Points of a Branching Diffusion Process
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Likelihood‐based inference of population history from low‐coverage de novo genome assemblies
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A Draft Sequence of the Neandertal Genome
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PHYLOGENIES FROM MOLECULAR SEQUENCES: INFERENCE AND RELIABILITY
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Natural hybridization in heliconiine butterflies: the species boundary as a continuum
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Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data
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A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species
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Inferring Demographic History from a Spectrum of Shared Haplotype Lengths
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Robust Demographic Inference from Genomic and SNP Data
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Genome-Wide Inference of Ancestral Recombination Graphs
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Multilocus Methods for Estimating Population Sizes, Migration Rates and Divergence Time, With Applications to the Divergence of Drosophila pseudoobscura and D. persimilis
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Estimating Divergence Parameters With Small Samples From a Large Number of Loci
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On Computing the Coalescence Time Density in an Isolation-With-Migration Model With Few Samples
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A General Method for Calculating Likelihoods Under the Coalescent Process
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Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes
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Inferring Bottlenecks from Genome-Wide Samples of Short Sequence Blocks
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