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Section: METHODS
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Fast and accurate estimation of selection coefficients and allele histories from ancient and modern DNA

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Andrew H Vaughn and Rasmus Nielsen
Molecular Biology and Evolution, msae156, https://doi.org/10.1093/molbev/msae156
Published: 30 July 2024
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Improving the accuracy of bulk fitness assays by correcting barcode processing biases

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Ryan Seamus McGee and others
Molecular Biology and Evolution, msae152, https://doi.org/10.1093/molbev/msae152
Published: 23 July 2024
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Polymorphism-Aware Models in RevBayes: Species Trees, Disentangling Balancing Selection, and GC-Biased Gene Conversion

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Svitlana Braichenko and others
Molecular Biology and Evolution, Volume 41, Issue 7, July 2024, msae138, https://doi.org/10.1093/molbev/msae138
Published: 09 July 2024
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Inference of Locus-Specific Population Mixtures from Linked Genome-Wide Allele Frequencies

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Carlos S Reyna-Blanco and others
Molecular Biology and Evolution, Volume 41, Issue 7, July 2024, msae137, https://doi.org/10.1093/molbev/msae137
Published: 03 July 2024
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PHACTboost: A Phylogeny-Aware Pathogenicity Predictor for Missense Mutations via Boosting

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Onur Dereli and others
Molecular Biology and Evolution, Volume 41, Issue 7, July 2024, msae136, https://doi.org/10.1093/molbev/msae136
Published: 27 June 2024
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Comparing Phylogeographies to Reveal Incompatible Geographical Histories within Genomes

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Benjamin Singer and others
Molecular Biology and Evolution, Volume 41, Issue 7, July 2024, msae126, https://doi.org/10.1093/molbev/msae126
Published: 26 June 2024
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Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning

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Sudip Sharma and Sudhir Kumar
Molecular Biology and Evolution, Volume 41, Issue 7, July 2024, msae131, https://doi.org/10.1093/molbev/msae131
Published: 25 June 2024
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COATi: Statistical Pairwise Alignment of Protein-Coding Sequences

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Juan José García Mesa and others
Molecular Biology and Evolution, Volume 41, Issue 7, July 2024, msae117, https://doi.org/10.1093/molbev/msae117
Published: 13 June 2024
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Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels

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Clara Iglhaut and others
Molecular Biology and Evolution, Volume 41, Issue 7, July 2024, msae109, https://doi.org/10.1093/molbev/msae109
Published: 06 June 2024
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The Tree Reconstruction Game: Phylogenetic Reconstruction Using Reinforcement Learning

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Dana Azouri and others
Molecular Biology and Evolution, Volume 41, Issue 6, June 2024, msae105, https://doi.org/10.1093/molbev/msae105
Published: 03 June 2024
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Boundary Effects Cause False Signals of Range Expansions in Population Genomic Data

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Petri Kemppainen and others
Molecular Biology and Evolution, Volume 41, Issue 5, May 2024, msae091, https://doi.org/10.1093/molbev/msae091
Published: 14 May 2024
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The Number and Pattern of Viral Genomic Reassortments are not Necessarily Identifiable from Segment Trees

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Qianying Lin and others
Molecular Biology and Evolution, Volume 41, Issue 6, June 2024, msae078, https://doi.org/10.1093/molbev/msae078
Published: 22 April 2024
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Computationally Efficient Demographic History Inference from Allele Frequencies with Supervised Machine Learning

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Linh N Tran and others
Molecular Biology and Evolution, Volume 41, Issue 5, May 2024, msae077, https://doi.org/10.1093/molbev/msae077
Published: 18 April 2024
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Comparison of Bayesian Coalescent Skyline Plot Models for Inferring Demographic Histories

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Ronja J Billenstein and Sebastian Höhna
Molecular Biology and Evolution, Volume 41, Issue 5, May 2024, msae073, https://doi.org/10.1093/molbev/msae073
Published: 17 April 2024
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fastDFE: Fast and Flexible Inference of the Distribution of Fitness Effects

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Janek Sendrowski and Thomas Bataillon
Molecular Biology and Evolution, Volume 41, Issue 5, May 2024, msae070, https://doi.org/10.1093/molbev/msae070
Published: 05 April 2024
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Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline

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Tobias Baril and others
Molecular Biology and Evolution, Volume 41, Issue 4, April 2024, msae068, https://doi.org/10.1093/molbev/msae068
Published: 05 April 2024
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Correlated Allele Frequency Changes Reveal Clonal Structure and Selection in Temporal Genetic Data

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Yunxiao Li and John P Barton
Molecular Biology and Evolution, Volume 41, Issue 4, April 2024, msae060, https://doi.org/10.1093/molbev/msae060
Published: 20 March 2024
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Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes Per Host

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Jake Carson and others
Molecular Biology and Evolution, Volume 41, Issue 1, January 2024, msad288, https://doi.org/10.1093/molbev/msad288
Published: 03 January 2024
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Transmission Bottleneck Size Estimation from De Novo Viral Genetic Variation

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Yike Teresa Shi and others
Molecular Biology and Evolution, Volume 41, Issue 1, January 2024, msad286, https://doi.org/10.1093/molbev/msad286
Published: 30 December 2023
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Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs

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Emma E Goldberg and others
Molecular Biology and Evolution, Volume 41, Issue 1, January 2024, msad282, https://doi.org/10.1093/molbev/msad282
Published: 27 December 2023