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Computational Phylogenetics

Peer-reviewed Journal Publications

1. Zhang, C., C. Scornavacca, E.K. Molloy, S. Mirarab, "ASTRAL-Pro: quartet-based species tree inference despite paralogy," Molecular Biology and Evolution, In press. [html] [code] [data]
2. Molloy, E.K. and T. Warnow, "FastMulRFS: Fast and highly accurate species tree estimation under generic gene duplication and loss models," Bioinformatics, 2020. [Special issue for ISMB 2020] [html] [code] [data]
3. Le, T., A. Sy, E.K. Molloy, Q. Zhang, S. Rao, and T. Warnow, "Using Constrained-INC for Large-scale Gene Tree and Species Tree Estimation," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2020. [Extended version of AlCoB 2019 paper] [html] [code]
4. Springer, M.S., E.K. Molloy, D.B. Sloan, M.P. Simmons, and J. Gatesy, "ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets," Journal of Heredity, 2020. [Editor's Choice] [html]
5. Christensen, S., E.K. Molloy, P. Vachaspati, A. Yammanuru, and T. Warnow, "Non-parametric correction of estimated gene trees using TRACTION," Algorithms for Molecular Biology, 2020. [Extended version of WABI 2019 paper] [html]
6. Molloy, E.K. and T. Warnow, "TreeMerge: A new method for improving the scalability of species tree estimation methods," Bioinformatics, 2019. [Special issue for ISMB 2019] [html] [code] [data]
7. Molloy, E.K. and T. Warnow, "Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge," Algorithms for Molecular Biology, 2019. [Extended version of RECOMB-CG 2018 paper] [html] [code] [data]
8. Nute, M., J. Chou, E.K. Molloy, and T. Warnow, "The Performance of Coalescent-Based Species Tree Estimation Methods under Models of Missing Data," BMC Genomics, 2018. [Extended version of RECOMB-CG 2017 paper] [html] [data]
9. Molloy, E.K. and T. Warnow, "To include or not to include: The Impact of Gene Filtering on Species Tree Estimation Methods," Systematic Biology, 2018. [html] [data]
10. Christensen, S., E.K. Molloy, P. Vachaspati, and T. Warnow, "OCTAL: Optimal completion of gene trees in polynomial time," Algorithms for Molecular Biology, 2018. [Extended version of WABI 2017 paper] [html] [code] [data]

Peer-reviewed Conference Proceedings

1. Yu, X., T. Le, S. Christensen, E.K. Molloy, and T. Warnow, "Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees," in 20th International Workshop on Algorithms and Bioinformatics. [WABI 2020] [html] [code]
2. Legried, B., E.K. Molloy, T. Warnow,and S. Roch, "Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss," in 24th International Conference on Research in Computational Molecular Biology. [RECOMB 2020] [html] [data]
3. Christensen, S., E.K. Molloy, P. Vachaspati, and T. Warnow, "TRACTION: Fast non-parametric improvement of estimated gene trees," in 19th International Workshop on Algorithms and Bioinformatics. [WABI 2019] [html] [code] [data]
4. Le, T., A. Sy, E.K. Molloy, Q. Zhang, S. Rao, and T. Warnow, "Using INC within Divide-and-Conquer Phylogeny Estimation," in 6th International Conference on Algorithms for Computational Biology. [AlCoB 2019] [html] [code] [data]
5. Molloy, E.K. and T. Warnow, "NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees," in 16th RECOMB International Conference on Comparative Genomics. [RECOMB-CG 2018] [html] [code] [data]
6. Christensen, S., E.K. Molloy, P. Vachaspati, and T. Warnow, "Optimal completion of incomplete gene trees in polynomial time using OCTAL," in 17th International Workshop on Algorithms and Bioinformatics. [WABI 2017] [html] [code] [data]

Book Chapters

1. Molloy, E.K. and T. Warnow. 2019. Large-scale Species Tree Estimation. Under revision. [Edited by Drs. Lacey Knowles and Laura Kubatko] [html]