On Reduced Amino Acid Alphabets for Phylogenetic Inference

Cited by (179)

Items 101–179 of 179

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4. Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics
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6. Genomics Reveals the Metabolic Potential and Functions in the Redistribution of Dissolved Organic Matter in Marine Environments of the Genus Thalassotalea
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12. RETRACTED: Integrative phylogenomics positions sponges at the root of the animal tree
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14. What is an archaeon and are the Archaea really unique?
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15. Repertoire-based diagnostics using statistical biophysics
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16. Available data do not rule out Ctenophora as the sister group to all other Metazoa
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17. A Test for Heterotachy Using Multiple Pairs of Sequences
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18. Inconsistent performance of multi‐type genomic data in phylogenomics of neuropteridan insects, with solutions toward conflicting results
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19. Revisiting the phylogenetic position of Caullerya mesnili (Ichthyosporea), a common Daphnia parasite, based on 22 protein-coding genes
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20. ORS‐Pred: An optimized reduced scheme‐based identifier for antioxidant proteins
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21. Archaea, the tree of life, and cellular evolution in eukaryotes
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22. Identification of Phase Separating Proteins With Distributed Reduced Alphabet Representations of Sequences
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23. State aggregation for fast likelihood computations in molecular evolution
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24. Measuring Historical and Compositional Signals in Phylogenetic Data
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25. Microbial Diversity and Open Questions about the Deep Tree of Life
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26. A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome
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27. BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more
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28. Diversity, ecology, cell biology and evolution of the Asgard archaea
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29. Alphabet reduction and distributed vector representation based method for classification of antimicrobial peptides
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30. The Roles of Protein Structure, Taxon Sampling, and Model Complexity in Phylogenomics: A Case Study Focused on Early Animal Divergences
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32. A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process Retained in Recoded DNA?
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33. Two fundamental questions about protein evolution
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34. On the group theoretical background of assigning stepwise mutations onto phylogenies
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35. Fast Statistical Tests for Detecting Heterotachy in Protein Evolution
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36. Simplification of complexity in protein molecular systems by grouping amino acids: a view from physics
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37. tRNA functional signatures classify plastids as late-branching cyanobacteria
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38. Detecting and visualising the impact of heterogeneous evolutionary processes on phylogenetic estimates
    Lars Sommer Jermiin, David R. Lovell, Bernhard Y. Misof, Peter Gordon Foster, John Robinson · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
39. Phylogenomic Analysis
    Andrew J. Roger, Martin Kolísko, Alastair G. B. Simpson · 2012 · Wiley eBooks
40. Phylogenomics and ancestral reconstruction of Korarchaeota reveals genomic adaptation to habitat switching
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41. WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing
    Stephan Köstlbacher, Kassiani Panagiotou, Daniel Tamarit, Thijs J. G. Ettema · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
42. Reply to: Available data do not rule out Ctenophora as the sister group to all other Metazoa
    Anthony K. Redmond, Aoife McLysaght · 2023 · Nature Communications
43. iProps: A Comprehensive Software Tool for Protein Classification and Analysis With Automatic Machine Learning Capabilities and Model Interpretation Capabilities
    Changli Feng, Haiyan Wei, Chugui Xu, Bin Feng, Xiaorong Zhu, Jing Liu, Quan Zou · 2024 · IEEE Journal of Biomedical and Health Informatics
44. Asgardarchaeota – A Novel Prokaryotic Group Discovered in Aquatic Sediments that Might Shed Light on the Origin and Early Evolution of Eukaryotes.
    Paul‐Adrian Bulzu, Adorján Cristea, Doriana M. Buda, Horia Leonard Banciu · 2019 · Aerul şi apa, componente ale mediului
45. Immunoglobulin Classification Based on FC* and GC* Features
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46. The Application of Data Compression-Based Distances to Biological Sequences
    Attila Kertész‐Farkas, András Kocsor, Sándor Pongor · 2008 · Information Theory and Statistical Learning
47. Reduced protein sequence patterns in identifying key structural elements of dissimilatory sulfite reductase homologs
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48. Early Divergence and Gene Exchange Highways in the Evolutionary History of Mesoaciditogales
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49. Machine Learning for Protein Function
    Dan Ofer · 2016 · arXiv (Cornell University)
50. Genomic remnants of ancestral hydrogen and methane metabolism in Archaea drive anaerobic carbon cycling
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51. Morphological data, phylogenomics and recalcitrant nodes
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52. The Dayhoff Exchange Score: A New Metric to Quantify Entropic Site Saturation in Amino Acid Data Sets Prior to Phylogenetic Analysis
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53. 古菌、生命树和真核细胞的功能演化
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54. Ubiquity and Origins of Structural Maintenance of Chromosomes (SMC) Proteins in Eukaryotes
    Mari Yoshinaga, Yuji Inagaki · 2021 · Institutional Repositories DataBase (IRDB)
55. State aggregation for fast likelihood computations in molecular evolution
    Iakov I. Davydov, Marc Robinson‐Rechavi, Nicolas Salamin · 2015 · bioRxiv (Cold Spring Harbor Laboratory)
56. Undinarchaeota illuminate the evolution of DPANN archaea
    Nina Dombrowski, T. Williams, Jiarui Sun, B. Woodcroft, Jun-Hoe Lee, M. Bui, C. Rinke, A. Spang · 2020 · bioRxiv
57. Ubiquity and origins of structural maintenance of chromosomes (SMC) proteins in eukaryotes
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58. Phylogénomique des structures multiprotéiques eucaryotes impliquées dans le cycle cellulaire et contribution à la phylogénie des eucaryotes.
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59. On the group theoretical background of assigning stepwise mutations onto
    Minh Anh Nguyen, Arndt von Haeseler · 2012
60. Peer Review #1 of "What is an archaeon and are the Archaea really unique? (v0.1)"
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61. Peer Review #1 of "What is an archaeon and are the Archaea really unique? (v0.2)"
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62. The ups and downs of amino acid co-evolution: evolutionary Stokes and anti-Stokes shifts
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63. Evolutionary dynamics under a stability-constrained model
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64. Hydropathy and Conformational Similarity-Based Distributed Representation of Protein Sequences for Properties Prediction
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65. Faculty Opinions recommendation of Revisiting metazoan phylogeny with genomic sampling of all phyla.
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66. Peer Review #2 of "What is an archaeon and are the Archaea really unique? (v0.1)"
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67. Peer Review #3 of "What is an archaeon and are the Archaea really unique? (v0.1)"
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68. Early divergence and gene exchange highways in the evolutionary history of Mesoaciditogales
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69. Nucleomorph phylogenomics suggests a deep and ancient origin of cryptophyte plastids within Rhodophyta
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70. Protein Classiflcation in a Machine Learning Framework
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71. Clarifying Xenacoelomorpha phylogeny: A polarized quartet-based analysis with SeaLion
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72. Impact des violations des modèles d'annotation et d'évolution de séquences en phylogénomique : application à l'étude des eucaryotes photosynthétiques
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73. Phylogenomic study of the evolutionary history of the Archaea and their link with eukaryogenesis
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74. Deep eukaryotic phylogenomics : the holomycota branch
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75. The evolution of red algal organellar genomes and the origin of red complex plastids
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76. kamino: fast proteome-wide variant calling for amino acid phylogenomics
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77. Constructive neutral evolution explains the emergence of specialised ribosomes in diverse eukaryotes
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78. A hidden archaeal lineage with an ultra-reduced genome retaining only its replicative core
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79. Data from: Phylogenomics of Lophotrochozoa with consideration of systematic error
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