Molecular Evolution and Phylogenetics

Nei M, Kumar S (2000)
Oxford University Press (333 pp.)

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Phylogenetic Trees Made Easy: A How-To Manual, Fifth Edition

Hall B (2017)
Sinauer Associates Inc, Sunderland (282 pp.)

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MEGA: Molecular Evolutionary Genetics Analysis version 1.01

Kumar S, Tamura K, Nei M (1993)
The Pennsylvania State University (135 pp.)

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MEGA-GPT: Artificial Intelligence Guidance and Building Analytical Protocols using MEGA software

MEGA-GPT: Artificial Intelligence Guidance and Building Analytical Protocols using MEGA software (2025)
Molecular Biology and Evolution (in review):

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MEGA Software Celebrates Silver Anniversary

MEGA Software Celebrates Silver Anniversary (2018)
Molecular Biology and Evolution 35:1558-1560

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Building Phylogenetic Trees from Molecular Data With MEGA

Building Phylogenetic Trees from Molecular Data With MEGA (2013)
Molecular Biology and Evolution 30:1229-1235

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Estimating TimeTrees with MEGA and the TimeTree Resource

Estimating TimeTrees with MEGA and the TimeTree Resource (2018)
Molecular Biology and Evolution 35:2334-2342

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A Protocol for Diagnosing the Effect of Calibration Priors on Posterior Time Estimates: A Case Study for the Cambrian Explosion of Animal Phyla

A Protocol for Diagnosing the Effect of Calibration Priors on Posterior Time Estimates: A Case Study for the Cambrian Explosion of Animal Phyla (2015)
Molecular Biology and Evolution 32:1907-1912

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Bootstrap and Rogue Identification Tests for Phylogenetic Analyses

Bootstrap and Rogue Identification Tests for Phylogenetic Analyses (2018)
Molecular Biology and Evolution 25:2327-2333

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Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times

Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times (2020)
Molecular Biology and Evolution 37:280-290

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A new method for inferring timetrees from temporally sampled molecular sequences

A new method for inferring timetrees from temporally sampled molecular sequences (2020)
PLoS Computational Biology 16:24pp

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A machine learning method for detecting autocorrelation of evolutionary rates in large phylogenies

A machine learning method for detecting autocorrelation of evolutionary rates in large phylogenies (2019)
Molecular Biology and Evolution 36:811-824

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Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates

Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates (2018)
Molecular Biology and Evolution 35:1770-1782

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RelTime relaxes the strict molecular clock throughout the phylogeny

RelTime relaxes the strict molecular clock throughout the phylogeny (2018)
Genome Biology and Evolution 10:1631-1636

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On estimating evolutionary probabilities of population variants

On estimating evolutionary probabilities of population variants (2019)
BMC Evolutionary Biology 19:133(14pp)

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