Pitfalls in supermatrix phylogenomics

Cited by (173)

Items 101–173 of 173

1. Microbial Diversity and Open Questions about the Deep Tree of Life
   Laura Eme, Daniel Tamarit · 2024 · Genome Biology and Evolution
2. Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population
   Lin Zhang Cheng, Mengge Li, Yachao Wang, Qunwei Han, Yanlin Hao, Zhen Qiao, Wei Zhang, Lin Qiu, An‐Dong Gong, Zhihan Zhang et al. · 2023 · Frontiers in Plant Science
3. CactEcoDB: Trait, spatial, environmental, phylogenetic and diversification data for the cactus family
   Jamie B. Thompson, Catherine Martinez, Jorge Avaria‐Llautureo, Santiago Ramírez‐Barahona, Gerardo Manzanarez-Villasana, Alastair Culham, Andrew Gdaniec, George Ryan, Chris Venditti, Georgia Keeling et al. · 2026 · Scientific Data
4. Exclusion of fast evolving genes or fast evolving sites produces different archaean phylogenies
   Ashley A. Superson, Fabia Ursula Battistuzzi · 2022 · Molecular Phylogenetics and Evolution
5. Patchwork: Alignment-Based Retrieval and Concatenation of Phylogenetic Markers from Genomic Data
   Felicia Sandberg, Clara G Köhne, Christoph Bleidorn · 2023 · Genome Biology and Evolution
6. Molecular evolution and morphological diversification of ulvophytes (Chlorophyta)
   Andrea Del Cortona, Frédérik Leliaert · 2017 · Perspectives in Phycology
7. A Time-calibrated Firefly (Coleoptera: Lampyridae) Phylogeny: Using Genomic Data for Divergence Time Estimation
   Sebastian Höhna, Sarah E. Lower, Pablo Duchen, Ana Catalán · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
8. Chloroplast phylogenomics of unicellular and colonial Volvocales provides perspectives on the evolution of morphological characters
   Xi Li, Xuan Shi, Hong Cheng, Shi-Yu Zhang, Zhi-Ping Yang, Xiao-Ya Ma, Bo‐Jian Zhong · 2022 · Journal of Systematics and Evolution
9. Assessing sequence heterogeneity in Chlorellaceae DNA barcode markers for phylogenetic inference
   E. Wong, Nurhaida Kamaruddin, Marina Mokhtar, Norjan Yusof, Raja Farhana Raja Khairuddin · 2023 · Journal of Genetic Engineering and Biotechnology
10. Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes
    Sandra Regina Maruyama, Luana Aparecida Rogerio, Patrícia Domingues de Freitas, Marta Maria Geraldes Teixeira, José M. C. Ribeiro · 2021 · Scientific Reports
11. Systematic position of the Clicking Frog (Kassinula Laurent, 1940), the problem of chimeric sequences and the revised classification of the family Hyperoliidae
    Tadeáš Nečas, Jos Kielgast, Zoltán T. Nagy, Chifundera Kusamba, Václav Gvoždík · 2022 · Molecular Phylogenetics and Evolution
12. Gene flow can reveal ghost lineages
    Théo Tricou, Enzo Marsot, Bastien Boussau, Éric Tannier, Damien M. de Vienne · 2025 · Evolutionary Journal of the Linnean Society
13. Branch Length Transforms using Optimal Tree Metric Matching
    Shayesteh Arasti, Puoya Tabaghi, Yasamin Tabatabaee, Alan Mayer, Siavash Mirarab · 2026 · Systematic Biology
14. Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny usingMycobacterium tuberculosisisolates
    Afif Elghraoui, Siavash Mirarab, Krister M. Swenson, Faramarz Valafar · 2023 · Bioinformatics
15. Disclosing the hidden nucleotide sequences: a journey into DNA barcoding of raptor species in public repositories
    Wattanawan Jaito, Jumaporn Sonongbua, Thitipong Panthum, Pish Wattanadilokchatkun, Nattakan Ariyaraphong, Thanyapat Thong, Worapong Singchat, Syed Farhan Ahmad, Ekaphan Kraichak, Narongrit Muangmai et al. · 2023 · Genes & Genomics
16. Scope for sympatric giant-dwarf speciation driven by cannibalism in South-American annual killifish ( Austrolebias )
    Tom J. M. Van Dooren, Henri A Thomassen, Femmie Smit, Andrew J. Helmstetter, Vincent Savolainen · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
17. Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships
    Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab · 2021 · SSRN Electronic Journal
18. Extreme genome scrambling in cryptic Oikopleura dioica species
    Charles Plessy, Michael J. Mansfield, Aleksandra Bliznina, Aki Masunaga, Charlotte West, Yongkai Tan, Andrew W. Liu, Jan Grašič, María Sara del Río Pisula, Gaspar Sánchez-Serna et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
19. Phylogenomic analysis of brachyuran crabs using transcriptome data reveals possible sources of conflicting phylogenetic relationships within the group
    Da Pan, Yunlong Sun, Boyang Shi, Ruxiao Wang, Peter K. L. Ng, Danièle Guinot, Neil Cumberlidge, Hongying Sun · 2024 · Molecular Phylogenetics and Evolution
20. TransMCL enables the assembly of full‐length coding genes for collecting complete hierarchical orthogroups
    Jingting Shen, Shengyu Zhou, Yamao Chen, Ji Qi · 2023 · Methods in Ecology and Evolution
21. Present and future of the study on Korean land planarians (Platyhelminthes: Tricladida: Geoplanidae)
    Ji–Hun Song, Fernando Carbayo · 2024 · Zoologia (Curitiba)
22. Overtraining often results in topologically incorrect species trees with maximum likelihood methods
    Damien M. de Vienne, Fran Supek, Toni Gabaldón · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
23. Phylogeny and Evolution of Vascular Plants
    Yin‐Long Qiu · 2018 · Encyclopedia of Life Sciences
24. Species delimitation in the grey zone: introgression obfuscates phylogenetic inference and species boundaries in a cryptic frog complex (Ranidae: Pulchrana picturata )
    Kin Onn Chan, Carl R. Hutter, Perry L. Wood, L. Lee Grismer, Rafe M. Brown · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
25. Evaluating Impacts of Syntenic Block Detection Strategies on Rearrangement Phylogeny Using M. tuberculosis Isolates
    Afif Elghraoui, Siavash Mirarab, Krister M. Swenson, Faramarz Valafar · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
26. Alignment-free Phylogenetic Placement and its Applications
    Matthias Blanke · 2023
27. Phylogenomics and comparative genomics in ant-eating mammals
    Rémi Allio · 2021 · theses.fr (ABES)
28. Tracing ancient life through the genomic record
    Morgan S. Sobol, Carolina A. Martínez-Gutiérrez · 2026 · Journal of Applied Microbiology
29. Detecting Outlier Subtrees of Gene Trees Using SPR Moves and Machine Learning
    Alan Mayer, Shayesteh Arasti, Siavash Mirarab · 2026 · Lecture notes in computer science
30. Introduction: Carving Nature at Its Joints, or Why Birds Are Not Dinosaurs and Men Are Not Apes
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
31. Beyond Classification
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
32. Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies
    Qiyun Zhu, Siavash Mirarab · 2022 · Methods in molecular biology
33. Tree Evaluation and Robustness Testing
    Mahendra Mariadassou, Avner Bar‐Hen, Hirohisa Kishino · 2018 · Elsevier eBooks
34. The impact of incongruence and exogenous gene fragments on estimates of the eukaryote root
    Caesar Al Jewari, S. Baldauf · 2021 · bioRxiv
35. OBSOLETE: Phylogenomics of Foodborne Pathogens: The Case of Listeria monocytogenes
    António Lourenço · 2015 · Elsevier eBooks
36. What This Book Is About
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
37. The world of molecular data is not enough – we still need more algal ultrastructure
    Linda Edwards Graham · 2017 · Journal of Phycology
38. Peer Review #1 of "Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics (v0.1)"
    2019 · PeerJ
39. Peer Review #1 of "Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics (v0.2)"
    2019 · PeerJ
40. Peer Review #2 of "Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics (v0.1)"
    2019 · PeerJ
41. Phylogenomics of Foodborne Pathogens: The Case of Listeria monocytogenes
    António Lourenço, KIERAN N JORDAN, Olivia E. McAuliffe · 2020 · Elsevier eBooks
42. Beyond Classification: How to Study Phylogeny
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
43. Essentialism and Typology
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
44. The Cladistic Programme
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
45. How to Study Classification
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
46. Systematics: Exposing Myths
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
47. How to Study Classification: Consensus Techniques and General Classifications
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
48. Parameters of Classification:Ordo Ab Chao
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
49. The Separation of Classification and Phylogenetics
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
50. Monothetic and Polythetic Taxa
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
51. Systematics Association Special Volumes
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cladistics
52. The Interrelationships of Organisms
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
53. Relationship Diagrams
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
54. Further Myths and More Misunderstandings
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
55. Non-taxa or the Absence of –Phyly: Paraphyly and Aphyly
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
56. How to Study Classification: ‘Total Evidence’ vs. ‘Consensus’, Character Congruence vs. Taxonomic Congruence, Simultaneous Analysis vs. Partitioned Data
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
57. Preface
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cladistics
58. Modern Artificial Methods and Raw Data
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
59. How to Study Classification
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
60. How to Study Classification
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
61. Classification
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
62. Afterword
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cladistics
63. Peer Review #3 of "Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics (v0.1)"
    2019 · PeerJ
64. Peer Review #3 of "Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics (v0.2)"
    2019 · PeerJ
65. Index
    David Mervyn Williams, Malte Christian Ebach · 2020 · Cambridge University Press eBooks
66. Robust phylogenomic inference through genome skimming as demonstrated by a systematic analysis of Nereididae
    Carl Roger Felix Thalén · 2022
67. Assembling an illustrated family‐level tree of life for exploration in mobile devices
    Andrés A. Del Risco, Diego A. Chacón, Lucia Ángel, David A. García · 2024 · Journal of Systematics and Evolution
68. Tree Evaluation and Robustness Testing
    Mahendra Mariadassou, Avner Bar‐Hen, Hirohisa Kishino · 2019 · Elsevier eBooks
69. Evolution et coévolution des petits ARNs régulateurs et des gènes codants chez les bactéries
    Franck Cerutti · 2018
70. Phylogenomic study of the evolutionary history of the Archaea and their link with eukaryogenesis
    Monique Aouad · 2018
71. Taxonomie intégrative, phylogénie et diversification des Turridae (Gastropoda, Conoidea)
    Paul Zaharias · 2019 · theses.fr (ABES)
72. Approche phylogénomique de la dynamique spatiale et temporelle de diversification chez les Lépidoptères Saturniidae
    Pierre Arnal · 2020
73. Vasal budding : characterization of a new form of non-embryonic development in the colonial ascidian Polyandrocarpa zorritensis
    Marta Scelzo · 2020