| 42 | MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods | |
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| 43 | MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 | |
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| 46 | MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets | |
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| 66 | MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability | |
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| 2013/01/16 | English | 25,711 |
| 90 | MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms | |
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| 2018/05/02 | English | 22,716 |
| 91 | MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0 | |
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| 2007/04/18 | English | 22,622 |
| 137 | MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space | |
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| 138 | CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP | |
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| 1985/07/01 | English | 17,750 |
| 230 | Confidence Limits on Phylogenies: An Approach Using the Bootstrap | |
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| 1985/07/01 | | 13,499 |
| 238 | IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies | |
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| 2014/11/03 | English | 13,279 |
| 245 | A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood | |
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| 2003/10/01 | English | 13,126 |
| 270 | New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 | |
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| 2010/03/29 | English | 12,462 |
| 346 | GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism | |
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| 1995/05/01 | English | 10,753 |
| 484 | PAML 4: Phylogenetic Analysis by Maximum Likelihood | |
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| 2007/04/18 | English | 8,963 |
| 549 | Median-joining networks for inferring intraspecific phylogenies | |
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| 1999/01/01 | English | 8,491 |
| 594 | jModelTest: Phylogenetic Model Averaging | |
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| 2008/04/03 | English | 8,158 |
| 639 | Bayesian Phylogenetics with BEAUti and the BEAST 1.7 | |
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| 2012/02/25 | English | 7,828 |
| 691 | Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis | |
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| 2000/04/01 | English | 7,445 |
| 809 | A general and simple method for obtaining R2 from generalized linear mixed‐effects models | |
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| 2012/12/03 | English | 6,841 |
| 836 | Phylogenies and the Comparative Method | |
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| 1985/01/01 | English | 6,729 |