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Molecular Phylogenetics and Evolution|April 23, 2016
Biases of tree-independent-character-subsampling methodsMark P Simmons, John Gatesy
Molecular Phylogenetics and Evolution|May 24, 2015
Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiospermsMark P Simmons, John Gatesy
Molecular Phylogenetics and Evolution|February 5, 2021
Collapsing dubiously resolved gene-tree branches in phylogenomic coalescent analysesMark P Simmons, John Gatesy
Molecular Phylogenetics and Evolution|November 8, 2021
Gene-tree misrooting drives conflicts in phylogenomic coalescent analyses of palaeognath birdsMark P Simmons, Mark S Springer, John Gatesy
Molecular Phylogenetics and Evolution|January 16, 2016
The effects of subsampling gene trees on coalescent methods applied to ancient divergencesMark P Simmons, Daniel B Sloan, John Gatesy
Molecular Phylogenetics and Evolution|November 5, 2018
Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analysesMark P Simmons, Daniel B Sloan, Mark S Springer, et al.
The Journal of Heredity|December 15, 2019
ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using QuartetsMark S Springer, Erin K Molloy, Daniel B Sloan, et al.
Cladistics : the International Journal of the Willi Hennig Society|April 25, 2023
Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analysesMark P Simmons, Pablo A Goloboff, Ben C Stöver, et al.
Cladistics : the International Journal of the Willi Hennig Society|October 30, 2021
Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family-level tree for MammaliaJohn Gatesy, Robert W Meredith, Jan E Janecka, et al.
Molecular Phylogenetics and Evolution|June 22, 2019
Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflictsJohn Gatesy, Daniel B Sloan, Jessica M Warren, et al.
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