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A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics

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journal contribution
posted on 2023-05-20, 19:26 authored by Jermiin, LS, Catullo, RA, Barbara HollandBarbara Holland
Molecular phylogenetics plays a key role in comparative genomics and has increasingly significant impacts on science, industry, government, public health and society. In this paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness of fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.


Publication title

NAR Genomics and Bioinformatics






School of Natural Sciences


Oxford University Press

Place of publication

United Kingdom

Rights statement

Copyright 2020 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (,

Repository Status

  • Open

Socio-economic Objectives

Expanding knowledge in the biological sciences

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