Species sampling has a major impact on phylogenetic inference

G Lecointre, H Philippe, HL Vân Lê… - Molecular phylogenetics …, 1993 - Elsevier
… underlying data and the method used to infer phylogenies. If molecular synapomorphies
defining a … of the data set used for phylogenetic inference but also roughly reflect the richness of …

The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy

AR Nabhan, IN Sarkar - Briefings in bioinformatics, 2012 - academic.oup.com
… sampling in phylogenetic inference experiments. This review summarizes progress to
date in understanding the impact of taxon sampling on the accuracy of phylogenetic analysis. …

The prevalence and impact of model violations in phylogenetic analysis

S Naser-Khdour, BQ Minh, W Zhang… - Genome biology and …, 2019 - academic.oup.com
… to evaluate the effect violating SRH conditions on phylogenetic inference. Our results suggest
that violating SRH assumptions can have substantial impacts on phylogenetic inference. …

Impacts of terraces on phylogenetic inference

MJ Sanderson, MM McMahon, A Stamatakis… - Systematic …, 2015 - academic.oup.com
… , particularly in settings where inference is already … about terraces and their impacts on
phylogenetic inference. First, we clarify … Third, we highlight the impact of terrace size on bootstrap …

Quantifying the impact of dependent evolution among sites in phylogenetic inference

CA Nasrallah, DH Mathews… - Systematic Biology, 2011 - academic.oup.com
… bias phylogenetic estimates. Here we quantify how robust methods of phylogenetic inference
… we evaluate the performance of traditional phylogenetic methods on these simulated data …

[HTML][HTML] Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference

B Roure, H Philippe - BMC evolutionary biology, 2011 - Springer
… time and its possible impact on phylogenetic inference. We used … to an erroneous phylogenetic
tree, we analyzed a concatenation of … can negatively influence phylogenetic inference. …

[HTML][HTML] Phylogenetic inference

M Haber, J Velasco - 2021 - seop.illc.uva.nl
… of selection may impact how we study or draw inferences about evolutionary processes, how
we identify the units of divergence and diversification will impact how we draw inferences in …

The effects of partitioning on phylogenetic inference

D Kainer, R Lanfear - Molecular Biology and Evolution, 2015 - academic.oup.com
… scheme choice on phylogenetic inference, we need to … of partitioning scheme choice on
phylogenetic inference by analyzing a … the impact of partitioning scheme choice on phylogenetic

The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow‐mouthed frogs (Anura, Microhylidae)

PLV Peloso, DR Frost, SJ Richards, MT Rodrigues… - …, 2016 - Wiley Online Library
… Our approach comprises an exploration of two distinct methods for phylogenetic inference
[parsimony and maximum likelihood (ML)] and five different data matrices (varying from 48 …

Data exploration in phylogenetic inference: scientific, heuristic, or neither

T Grant, AG Kluge - Cladistics, 2003 - Wiley Online Library
… relevance of data exploration to phylogenetic inference has yet to be … of phylogenetic
inference? Our reason for seeking answers to these questions is that for phylogenetic inference to …