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For: Haag J, Höhler D, Bettisworth B, Stamatakis A. From Easy to Hopeless-Predicting the Difficulty of Phylogenetic Analyses. Mol Biol Evol 2022;39:6832260. [PMID: 36395091 PMCID: PMC9728795 DOI: 10.1093/molbev/msac254] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Jin XJ, Yu Y, Lin HY, Liu FL, Wang HF, Ma Q, Chen Y, Zhang YH, Li P. Revisiting the backbone phylogeny and inferring the evolutionary trends in inflorescence of Elsholtzieae (Lamiaceae): new insights from orthologous nuclear genes. Cladistics 2025;41:157-176. [PMID: 39966307 DOI: 10.1111/cla.12604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 12/08/2024] [Accepted: 12/11/2024] [Indexed: 02/20/2025]  Open
2
Collienne L, Barker M, Suchard MA, Matsen FA. Phylogenetic Tree Instability After Taxon Addition: Empirical Frequency, Predictability, and Consequences For Online Inference. Syst Biol 2025;74:101-111. [PMID: 39453463 PMCID: PMC11809580 DOI: 10.1093/sysbio/syae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 09/30/2024] [Accepted: 10/22/2024] [Indexed: 10/26/2024]  Open
3
Ren H, Wong TKF, Minh BQ, Lanfear R. MixtureFinder: Estimating DNA Mixture Models for Phylogenetic Analyses. Mol Biol Evol 2025;42:msae264. [PMID: 39715360 PMCID: PMC11704958 DOI: 10.1093/molbev/msae264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 11/26/2024] [Accepted: 12/19/2024] [Indexed: 12/25/2024]  Open
4
Berling L, Bouckaert R, Gavryushkin A. An Automated Convergence Diagnostic for Phylogenetic MCMC Analyses. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:2246-2257. [PMID: 39255085 DOI: 10.1109/tcbb.2024.3457875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
5
Liu C, Zhou X, Li Y, Hittinger CT, Pan R, Huang J, Chen XX, Rokas A, Chen Y, Shen XX. The Influence of the Number of Tree Searches on Maximum Likelihood Inference in Phylogenomics. Syst Biol 2024;73:807-822. [PMID: 38940001 DOI: 10.1093/sysbio/syae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 06/29/2024]  Open
6
Wiegert J, Höhler D, Haag J, Stamatakis A. Predicting Phylogenetic Bootstrap Values via Machine Learning. Mol Biol Evol 2024;41:msae215. [PMID: 39418337 PMCID: PMC11523138 DOI: 10.1093/molbev/msae215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 08/28/2024] [Accepted: 09/15/2024] [Indexed: 10/19/2024]  Open
7
Charamis J, Balaska S, Ioannidis P, Dvořák V, Mavridis K, McDowell MA, Pavlidis P, Feyereisen R, Volf P, Vontas J. Comparative Genomics Uncovers the Evolutionary Dynamics of Detoxification and Insecticide Target Genes Across 11 Phlebotomine Sand Flies. Genome Biol Evol 2024;16:evae186. [PMID: 39224065 PMCID: PMC11412322 DOI: 10.1093/gbe/evae186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 08/09/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]  Open
8
Han Y, Xie Y, Hao Z, Mao J, Wang X, Chang Y, Tian Y. The Mitochondrial Genome of Ylistrum japonicum (Bivalvia, Pectinidae) and Its Phylogenetic Analysis. Int J Mol Sci 2024;25:8755. [PMID: 39201441 PMCID: PMC11354973 DOI: 10.3390/ijms25168755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/06/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024]  Open
9
Mo YK, Hahn MW, Smith ML. Applications of machine learning in phylogenetics. Mol Phylogenet Evol 2024;196:108066. [PMID: 38565358 DOI: 10.1016/j.ympev.2024.108066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/16/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
10
Ecker N, Huchon D, Mansour Y, Mayrose I, Pupko T. A machine-learning-based alternative to phylogenetic bootstrap. Bioinformatics 2024;40:i208-i217. [PMID: 38940166 PMCID: PMC11211842 DOI: 10.1093/bioinformatics/btae255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]  Open
11
Azouri D, Granit O, Alburquerque M, Mansour Y, Pupko T, Mayrose I. The Tree Reconstruction Game: Phylogenetic Reconstruction Using Reinforcement Learning. Mol Biol Evol 2024;41:msae105. [PMID: 38829798 PMCID: PMC11180600 DOI: 10.1093/molbev/msae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 05/17/2024] [Accepted: 05/28/2024] [Indexed: 06/05/2024]  Open
12
Stiller J, Feng S, Chowdhury AA, Rivas-González I, Duchêne DA, Fang Q, Deng Y, Kozlov A, Stamatakis A, Claramunt S, Nguyen JMT, Ho SYW, Faircloth BC, Haag J, Houde P, Cracraft J, Balaban M, Mai U, Chen G, Gao R, Zhou C, Xie Y, Huang Z, Cao Z, Yan Z, Ogilvie HA, Nakhleh L, Lindow B, Morel B, Fjeldså J, Hosner PA, da Fonseca RR, Petersen B, Tobias JA, Székely T, Kennedy JD, Reeve AH, Liker A, Stervander M, Antunes A, Tietze DT, Bertelsen MF, Lei F, Rahbek C, Graves GR, Schierup MH, Warnow T, Braun EL, Gilbert MTP, Jarvis ED, Mirarab S, Zhang G. Complexity of avian evolution revealed by family-level genomes. Nature 2024;629:851-860. [PMID: 38560995 PMCID: PMC11111414 DOI: 10.1038/s41586-024-07323-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
13
Morel B, Williams TA, Stamatakis A, Szöllősi GJ. AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss. Bioinformatics 2024;40:btae162. [PMID: 38514421 PMCID: PMC10990685 DOI: 10.1093/bioinformatics/btae162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/30/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024]  Open
14
Williams TA, Davin AA, Szánthó LL, Stamatakis A, Wahl NA, Woodcroft BJ, Soo RM, Eme L, Sheridan PO, Gubry-Rangin C, Spang A, Hugenholtz P, Szöllősi GJ. Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution. THE ISME JOURNAL 2024;18:wrae129. [PMID: 39001714 PMCID: PMC11293204 DOI: 10.1093/ismejo/wrae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/01/2024] [Accepted: 07/12/2024] [Indexed: 07/15/2024]
15
Trost J, Haag J, Höhler D, Jacob L, Stamatakis A, Boussau B. Simulations of Sequence Evolution: How (Un)realistic They Are and Why. Mol Biol Evol 2024;41:msad277. [PMID: 38124381 PMCID: PMC10768886 DOI: 10.1093/molbev/msad277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/17/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]  Open
16
Steenwyk JL, Li Y, Zhou X, Shen XX, Rokas A. Incongruence in the phylogenomics era. Nat Rev Genet 2023;24:834-850. [PMID: 37369847 PMCID: PMC11499941 DOI: 10.1038/s41576-023-00620-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2023] [Indexed: 06/29/2023]
17
Togkousidis A, Kozlov OM, Haag J, Höhler D, Stamatakis A. Adaptive RAxML-NG: Accelerating Phylogenetic Inference under Maximum Likelihood using Dataset Difficulty. Mol Biol Evol 2023;40:msad227. [PMID: 37804116 PMCID: PMC10584362 DOI: 10.1093/molbev/msad227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/06/2023] [Accepted: 09/26/2023] [Indexed: 10/08/2023]  Open
18
Kumar S, Tao Q, Lamarca AP, Tamura K. Computational Reproducibility of Molecular Phylogenies. Mol Biol Evol 2023;40:msad165. [PMID: 37467477 PMCID: PMC10370456 DOI: 10.1093/molbev/msad165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]  Open
19
Cokelaer T, Cohen-Boulakia S, Lemoine F. Reprohackathons: promoting reproducibility in bioinformatics through training. Bioinformatics 2023;39:i11-i20. [PMID: 37387150 DOI: 10.1093/bioinformatics/btad227] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]  Open
20
Černý D, Simonoff AL. Statistical evaluation of character support reveals the instability of higher-level dinosaur phylogeny. Sci Rep 2023;13:9273. [PMID: 37286556 DOI: 10.1038/s41598-023-35784-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/23/2023] [Indexed: 06/09/2023]  Open
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