Statistical binning enables an accurate coalescent-based estimation of the avian tree

Cited by (256)

Items 201–256 of 256

1. The effect of gene tree dependence on summary methods for species tree inference
   Wan-Ting He, Céline Scornavacca, Yao-ban Chan · 2026 · Peer Community Journal
2. QuCo: quartet-based co-estimation of species trees and gene trees
   Maryam Rabiee, Siavash Mirarab · 2022 · Bioinformatics
3. Quartet-based inference of cell differentiation trees from ChIP-Seq histone modification data
   Nazifa Ahmed Moumi, Badhan Das, Zarin Tasnim Promi, Nishat Anjum Bristy, Md. Shamsuzzoha Bayzid · 2019 · PLoS ONE
4. Fast and accurate large multiple sequence alignments using root-to-leave regressive computation
   Edgar Garriga Nogales, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Hafid Laayouni, Fyodor A. Kondrashov, Evan W. Floden, Cédric Notredame · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
5. Phylogenomic terraces: presence and implication in species tree estimation from gene trees
   Ishrat Tanzila Farah, Md Muktadirul Islam, Kazi Tasnim Zinat, Atif Hasan Rahman, Md. Shamsuzzoha Bayzid · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
6. Comparative Genomics and Genome Evolution in birds-of-paradise
   Stefan Prost, Ellie E. Armstrong, Johan A. A. Nylander, Gregg W.C. Thomas, Alexander Suh, Bent Petersen, Love Dalén, Brett W. Benz, Mozes P. K. Blom, Eleftheria Palkopoulou et al. · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
7. Phylotranscriptomics provides insights into the Mesoproterozoic-Neoproterozoic origin and diversification of green algae Trebouxiophyceae
   Ting Wang, Huan Feng, Chengcheng Zhu, Runjie Diao, Bojian Zhong · 2025 · Cell Reports
8. On the Robustness to Gene Tree Rooting (or Lack Thereof) of Triplet-Based Species Tree Estimation Methods
   Tanjeem Azwad Zaman, Rabib Jahin Ibn Momin, Md. Shamsuzzoha Bayzid · 2025 · Lecture notes in computer science
9. QT-WEAVER: Correcting Quartet Distribution Improves Phylogenomic Analyses Despite Gene Tree Estimation Error
   Navid Bin Hasan, Sohaib, Md. Shamsuzzoha Bayzid · 2025 · Lecture notes in computer science
10. Phylotranscriptomics reveals conflicts of deep nodes in Saxifragales
    Huiling Li, Hong Chang, Huan Xie, Lei Zhang, Guo-Qian Hao, Dimitar Dimitrov, Peng-Chuan Sun, Nathanael Walker‐Hale, Jia-Liang Li, Xiao-Ting Xu · 2026 · Molecular Phylogenetics and Evolution
11. Ultraconserved elements, DNA barcoding and morphology unravel the diversity and evolution of the Hypoponera pruinosa group (Hymenoptera: Formicidae) in Indochina and the Indo-Australian region
    Wendy Y. Wang, Bonnie B. Blaimer, Weeyawat Jaitrong, S. Hosoishi, Seiki Yamane · 2026 · Insect Systematics and Diversity
12. Phylogenetic investigation and taxonomic revision of the subgenus Anguinum ( Allium , Amaryllidaceae) using multi-omics data
    Rui‐Yu Cheng, Jin‐Bo Tan, Deng‐Feng Xie, Xing‐Jin He · 2026 · Botanical Journal of the Linnean Society
13. Detecting Outlier Subtrees of Gene Trees Using SPR Moves and Machine Learning
    Alan Mayer, Shayesteh Arasti, Siavash Mirarab · 2026 · Lecture notes in computer science
14. Phylogenomics beyond the ‘bag-of-genes’ model
    Iker Rivas-González, Siavash Mirarab, Edward L. Braun · 2026 · Trends in Genetics
15. IDXL: Species Tree Inference Using Internode Distance and Excess Gene Leaf Count
    Sourya Bhattacharyya, Jayanta Mukherjee · 2017 · Journal of Molecular Evolution
16. Evolutionary genotype-phenotype systems biology and study on the ruminant evolution
    Lei Chen, Qiang Qiu, Xiangyu Pan, Wen Wang · 2019 · Scientia Sinica Vitae
17. Supergene validation: A model-based protocol for assessing the accuracy of non-model-based supergene methods
    Richard H. Jr. Adams, Todd A. Castoe · 2019 · MethodsX
18. PhyloWGA: chromosome-aware phylogenetic interrogation of whole genome alignments
    Richard H. Jr. Adams, Todd A. Castoe, Michael DeGiorgio · 2020 · Bioinformatics
19. O papel de transferência horizontal de genes na história evolutiva de duas classes de genes em bactérias
    Luiz Thibério Rangel · 2017 · Digital Library of Theses and Dissertations (Universidade de São Paulo)
20. When species trees disagree: an approach consistent with the coalescent that quantifies phylogenomic support for contentious relationships
    Richard G.J. Hodel, Joseph F. Walker, L. Lacey Knowles, Stephen A. Smith · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
21. Non-phylogenetic identification of co-evolving genes for reconstructing the archaeal Tree of Life
    Luiz Thibério Rangel, Shannon M. Soucy, João Carlos Setúbal, Johann Peter Gogarten, Gregory P. Fournier · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
22. COAL_PHYRE: A Composite Likelihood Method for Estimating Species Tree Parameters from Genomic Data Using Coalescent Theory
    Geno Guerra, Rasmus Nielsen · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
23. Whole-Genome Alignment and Comparative Annotation
    J. Armstrong, Ian T. Fiddes, M. Diekhans, B. Paten · 2018 · Annual Review of Animal Biosciences
24. TREE-QMC: Improving quartet graph construction for scalable and accurate species tree estimation from gene trees
    Yunheng Han, Erin K. Molloy · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
25. Differential Effects of Incomplete Lineage Sorting and Gene Tree Estimation Error on Gene Tree Distributions and Species Tree Inference
    Nafis Tahmid, Shattik Islam Rhythm, Md. Shamsuzzoha Bayzid · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
26. Scaling coalescent-based species tree inference to 100,000 taxa with STELAR-X
    A. Saha, Md. Shamsuzzoha Bayzid · 2026 · Genome Research
27. Environmental, Toxicological, and Evolutionary Influences on Membrane Composition in Fish
    Alexander Gonzalez · 2016 · uO Research (University of Ottawa)
28. C4 photosynthetic evolution : sub-types, diversity, and function within the grass tribe Paniceae
    Jacob D. Washburn · 2017
29. Species tree estimation using Neighbor Joining
    Joseph Rusinko, Matt McPartlon · 2016 · arXiv (Cornell University)
30. Evolution of Melicope J.R.Forst & G.Forst (Rutaceae), the largest adaptive radiation of woody plants on the Hawaiian Islands.
    Claudia Paetzold · 2020
31. Convergence of maximum likelihood supertree reconstruction
    Lam Si Tung Ho, Vu Dinh · 2021 · arXiv (Cornell University)
32. Convergence of maximum likelihood supertree reconstruction
    Vu Dinh, Lam Si Tung Ho · 2021 · AIMS Mathematics
33. Recent Progress on Methods for Estimating and Updating Large Phylogenies
    Paul Zaharias, Tandy J. Warnow · 2022 · Preprints.org
34. Peer Review #2 of "Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage (v0.1)"
    2016 · PeerJ
35. Peer Review #2 of "Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus (v0.3)"
    2019 · PeerJ
36. Peer Review #2 of "Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus (v0.1)"
    2019 · PeerJ
37. Peer Review #2 of "Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus (v0.2)"
    2019 · PeerJ
38. Peer Review #3 of "Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus (v0.3)"
    2019 · PeerJ
39. Peer Review #1 of "Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage (v0.1)"
    2016 · PeerJ
40. Peer Review #1 of "Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage (v0.2)"
    2016 · PeerJ
41. Peer Review #3 of "Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus (v0.1)"
    2019 · PeerJ
42. Faculty Opinions recommendation of One thousand plant transcriptomes and the phylogenomics of green plants.
    Stefan de Folter · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
43. Fast and Accurate Species Trees from Weighted Internode Distances
    Baqiao Liu, Tandy J. Warnow · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
44. QR-STAR: A Polynomial-Time Statistically Consistent Method for Rooting Species Trees Under the Coalescent
    Yasamin Tabatabaee, Sebastien Roch, Tandy Warnow · 2023 · Journal of Computational Biology
45. The Most Frequent Gene Tree Based on Phylogenomic Data Reveals Insights into the Origins of Land Vertebrates
    Yunfeng Shan, Xiaoliang Wang, Habib Ali, Yongsheng Xie, Lu-Wei Tang, Youjun Zhou · 2023 · International Conference on Computational Science and Computational Intelligence (CSCI)
46. Target enrichment phylogenomics and biogeographic analyses unravel rapid radiation and reticulate evolution between Hainan-South China mainland -Vietnam in Section Nintooa ( Lonicera , Caprifoliaceae)
    Shi-you Zuo, Qinghui Sun, Diego F. Morales‐Briones, Hong‐Xin Wang, Jacob B. Landis, Hongyang Li, Hongjin Dong, Jun Wen, Hua‐Feng Wang · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
47. The topography of gene tree topology space in a plant genus with a legacy of recent polyploidy and introgression
    Jacob B. Landis, Andrew D Farmer, Lucio Garcia, Racella J. McNair, Mariana Franco Ruiz, Qingli Liu, Jeff J. Doyle · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
48. Improvement to GLASS/Maximum Tree Method of Species Tree Inference Using Measurement Error Modified Single Linkage Clustering
    Sarah Alver, Fletcher Christensen, J. H. Degnan · 2025 · IEEE Transactions on Computational Biology and Bioinformatics
49. Two-step species tree inference under the multispecies coalescent using full-likelihood
    Wenjie Zhu, Sebastian Höhna · 2025 · Evolutionary Journal of the Linnean Society
50. Additional file 1 of Forcing external constraints on tree inference using ASTRAL
    Maryam Rabiee, Siavash Mirarab · 2020 · Figshare
51. Additional file 6 of Whole genome phylogeny of Gallus: introgression and data-type effects
    George P. Tiley, Akanksha Pandey, Rebecca T. Kimball, Braun, Edward L., J. Gordon Burleigh · 2020 · Figshare
52. Additional file 8 of Whole genome phylogeny of Gallus: introgression and data-type effects
    George P. Tiley, Akanksha Pandey, Rebecca T. Kimball, Braun, Edward L., J. Gordon Burleigh · 2020 · Figshare
53. Additional file 7 of Whole genome phylogeny of Gallus: introgression and data-type effects
    George P. Tiley, Akanksha Pandey, Rebecca T. Kimball, Braun, Edward L., J. Gordon Burleigh · 2020 · Figshare
54. STEQ: A statistically consistent quartet distance based species tree estimation method
    Prottoy Saha, Anik Kumar Saha, Mrinmoy Saha Roddur, Sagor Sikdar, Nayeem Hasan Anik, Rezwana Reaz, Md. Shamsuzzoha Bayzid · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
55. Taxonomie intégrative, phylogénie et diversification des Turridae (Gastropoda, Conoidea)
    Paul Zaharias · 2019 · theses.fr (ABES)
56. Structural Variant benchmarking frameworks: Parameterization, matching logic, and evaluation assumptions presented through HG002 and NA12878
    Gamze Maden, Mehmet Baysan, Nizamettin Aydın · 2026 · PLoS Computational Biology