| BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis R Bouckaert, et al. PLoS Computational Biology 15 (4), e1006650, 2019 | 3593 | 2019 |
| CAFE 5 models variation in evolutionary rates among gene families FK +Mendes, D +Vanderpool, B +Fulton, MW Hahn Bioinformatics 36 (22-23), 5516–5518, 2020 | 474 | 2020 |
| Gene tree discordance causes apparent substitution rate variation FK Mendes, MW Hahn Systematic Biology 65 (4), 711-721, 2016 | 178 | 2016 |
| Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand JL Geoghegan, X Ren, M Storey, J Hadfield, L Jelley, S Jefferies, ... Nature Communications 11 (6351), 2020 | 149 | 2020 |
| Why concatenation fails near the anomaly zone FK Mendes, MW Hahn Systematic Biology 67 (1), 158-169, 2018 | 131 | 2018 |
| Soft shoulders ahead: spurious signatures of soft and partial selective sweeps result from linked hard sweeps D Schrider, FK Mendes, MW Hahn, AD Kern Genetics 200 (1), 267-284, 2015 | 111 | 2015 |
| Gene tree discordance can generate patterns of diminishing convergence over time FK Mendes, Y Hahn, MW Hahn Molecular Biology and Evolution 33 (12), 3299-3307, 2016 | 68 | 2016 |
| A multispecies coalescent model for quantitative traits FK Mendes, JA Fuentes-González, J Schraiber, MW Hahn eLife 7, e36482, 2018 | 46 | 2018 |
| Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations J +Douglas, FK +Mendes, R Bouckaert, D Xie, CL Jimenez-Silva, ... Virus Evolution 7 (2), veab052, 2021 | 42 | 2021 |
| The perils of intralocus recombination for inferences of molecular convergence FK Mendes, AP Livera, MW Hahn Philosophical Transactions of the Royal Society B 374 (1777), 20180244, 2019 | 39 | 2019 |
| Genomic evidence of gene flow during reinforcement in Texas Phlox F Roda, FK Mendes, MW Hahn, R Hopkins Molecular Ecology 26 (8), 2317-2330, 2017 | 35 | 2017 |
| A multi‐platform package for the analysis of intra‐ and interspecific trait evolution T +Gaboriau, FK +Mendes, S Joly, D Silvestro, N Salamin Methods in Ecology and Evolution 11 (11), 1439-1447, 2020 | 18 | 2020 |
| Novel integrative modeling of molecules and morphology across evolutionary timescales HA +Ogilvie, FK +Mendes, TG Vaughan, NJ Matzke, T Stadler, D Welch, ... Systematic Biology 71 (1), 208-220, 2022 | 13 | 2022 |
| LinguaPhylo: a probabilistic model specification language for reproducible phylogenetic analyses AJ Drummond, K Chen, FK Mendes, D Xie PLoS Computational Biology 19 (7), e1011226, 2023 | 10 | 2023 |
| Fast Bayesian inference of phylogenies from multiple continuous characters R Zhang, AJ Drummond, FK +Mendes Systematic Biology 73 (1), 102-124, 2024 | 8 | 2024 |
| How to validate a Bayesian evolutionary model FK Mendes, R Bouckaert, LM Carvalho, AJ Drummond Systematic Biology 74 (1), 158-175, 2025 | 7 | 2025 |
| Fast Bayesian inference of phylogenies from multiple continuous characters R Zhang, AJ Drummond, FK +Mendes bioRxiv, 2021 | 5* | 2021 |
| PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models FK Mendes, MJ Landis Systematic Biology 73 (6), 1051-1060, 2024 | 1 | 2024 |
| Lessons learned from organizing and teaching virtual phylogenetics workshops J Barido-Sottani, JA Justison, R Borges, JM Brown, W Dismukes, ... Bulletin of the Society of Systematic Biologists 1 (2), 8425, 2022 | | 2022 |
Alexei J. DrummondProfessor of Computational Biology, University of AucklandVerified email at cs.auckland.ac.nz
