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For: Löytynoja A, Goldman N. Evolution. Uniting alignments and trees. Science 2009;324:1528-9. [PMID: 19541988 DOI: 10.1126/science.1175949] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Number Cited by Other Article(s)
1
Zhao R, Wang HH, Wang Z, Xiao X, Yin XH, Hu SY, Miao HN, Zhang YJ, Liang P, Gu SH. Omics Analysis of Odorant-Binding Proteins and Cuticle-Enriched SfruOBP18 Confers Multi-Insecticide Tolerance in Spodoptera frugiperda. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39373658 DOI: 10.1021/acs.jafc.4c05737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
2
Estevez-Castro CF, Rodrigues MF, Babarit A, Ferreira FV, de Andrade EG, Marois E, Cogni R, Aguiar ERGR, Marques JT, Olmo RP. Neofunctionalization driven by positive selection led to the retention of the loqs2 gene encoding an Aedes specific dsRNA binding protein. BMC Biol 2024;22:14. [PMID: 38273313 PMCID: PMC10809485 DOI: 10.1186/s12915-024-01821-4] [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: 02/07/2022] [Accepted: 01/10/2024] [Indexed: 01/27/2024]  Open
3
Chang JM, Floden EW, Herrero J, Gascuel O, Di Tommaso P, Notredame C. Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability. Bioinformatics 2019;37:1506-1514. [PMID: 30726875 PMCID: PMC8275982 DOI: 10.1093/bioinformatics/btz082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/12/2018] [Accepted: 02/05/2019] [Indexed: 12/30/2022]  Open
4
A Shepherd D, Klaere S. How Well Does Your Phylogenetic Model Fit Your Data? Syst Biol 2018;68:157-167. [DOI: 10.1093/sysbio/syy066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 10/11/2018] [Indexed: 12/27/2022]  Open
5
Bromham L, Duchêne S, Hua X, Ritchie AM, Duchêne DA, Ho SYW. Bayesian molecular dating: opening up the black box. Biol Rev Camb Philos Soc 2017;93:1165-1191. [DOI: 10.1111/brv.12390] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 11/13/2017] [Accepted: 11/17/2017] [Indexed: 12/27/2022]
6
Nascimento FF, Reis MD, Yang Z. A biologist's guide to Bayesian phylogenetic analysis. Nat Ecol Evol 2017;1:1446-1454. [PMID: 28983516 PMCID: PMC5624502 DOI: 10.1038/s41559-017-0280-x] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 07/17/2017] [Indexed: 11/09/2022]
7
Adato O, Ninyo N, Gophna U, Snir S. Detecting Horizontal Gene Transfer between Closely Related Taxa. PLoS Comput Biol 2015;11:e1004408. [PMID: 26439115 PMCID: PMC4595140 DOI: 10.1371/journal.pcbi.1004408] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 06/20/2015] [Indexed: 01/12/2023]  Open
8
Kasarda DD, Adalsteins E, Lew EJL, Lazo GR, Altenbach SB. Farinin: characterization of a novel wheat endosperm protein belonging to the prolamin superfamily. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013;61:2407-17. [PMID: 23414243 DOI: 10.1021/jf3053466] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
9
Tóth A, Hausknecht A, Krisai-Greilhuber I, Papp T, Vágvölgyi C, Nagy LG. Iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family Bolbitiaceae. PLoS One 2013;8:e56143. [PMID: 23418526 PMCID: PMC3572013 DOI: 10.1371/journal.pone.0056143] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 01/07/2013] [Indexed: 11/19/2022]  Open
10
Mello B, Schrago CG. Incorrect handling of calibration information in divergence time inference: an example from volcanic islands. Ecol Evol 2012;2:493-500. [PMID: 22822429 PMCID: PMC3399139 DOI: 10.1002/ece3.94] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 11/25/2011] [Accepted: 11/29/2011] [Indexed: 11/21/2022]  Open
11
Bayzid MDS, Warnow T. Estimating Optimal Species Trees from Incomplete Gene Trees Under Deep Coalescence. J Comput Biol 2012;19:591-605. [DOI: 10.1089/cmb.2012.0037] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
12
Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning APJ, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci 2012;21:769-85. [PMID: 22528593 PMCID: PMC3403413 DOI: 10.1002/pro.2071] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 03/22/2012] [Accepted: 03/23/2012] [Indexed: 12/20/2022]
13
Löytynoja A, Vilella AJ, Goldman N. Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. ACTA ACUST UNITED AC 2012;28:1684-91. [PMID: 22531217 PMCID: PMC3381962 DOI: 10.1093/bioinformatics/bts198] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
14
Kawrykow A, Roumanis G, Kam A, Kwak D, Leung C, Wu C, Zarour E, Sarmenta L, Blanchette M, Waldispühl J. Phylo: a citizen science approach for improving multiple sequence alignment. PLoS One 2012;7:e31362. [PMID: 22412834 PMCID: PMC3296692 DOI: 10.1371/journal.pone.0031362] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 01/09/2012] [Indexed: 01/07/2023]  Open
15
Koskela M, Annila A. Looking for the Last Universal Common Ancestor (LUCA). Genes (Basel) 2012;3:81-7. [PMID: 24704844 PMCID: PMC3899962 DOI: 10.3390/genes3010081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 12/18/2011] [Accepted: 12/29/2011] [Indexed: 11/22/2022]  Open
16
Löytynoja A. Alignment methods: strategies, challenges, benchmarking, and comparative overview. Methods Mol Biol 2012;855:203-35. [PMID: 22407710 DOI: 10.1007/978-1-61779-582-4_7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
17
Can sensitivity analysis help to detect long-branch attraction? Mol Phylogenet Evol 2011;61:899-903. [DOI: 10.1016/j.ympev.2011.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 08/01/2011] [Accepted: 08/04/2011] [Indexed: 11/19/2022]
18
Yang ZL. Molecular techniques revolutionize knowledge of basidiomycete evolution. FUNGAL DIVERS 2011. [DOI: 10.1007/s13225-011-0121-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
19
Wang Z, Nilsson RH, Lopez-Giraldez F, Zhuang WY, Dai YC, Johnston PR, Townsend JP. Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data. PLoS One 2011;6:e19039. [PMID: 21533038 PMCID: PMC3080880 DOI: 10.1371/journal.pone.0019039] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 03/22/2011] [Indexed: 12/14/2022]  Open
20
Sipos B, Massingham T, Jordan GE, Goldman N. PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment. BMC Bioinformatics 2011;12:104. [PMID: 21504561 PMCID: PMC3102636 DOI: 10.1186/1471-2105-12-104] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 04/19/2011] [Indexed: 11/10/2022]  Open
21
Lam TTY, Hon CC, Tang JW. Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections. Crit Rev Clin Lab Sci 2010;47:5-49. [PMID: 20367503 DOI: 10.3109/10408361003633318] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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