A. Stamatakis

The power and limitations of species tree-aware phylogenetics

This paper reviews species tree-aware phylogenetic methods, evaluates their reliability, and discusses their applications and limitations in inferring gene and species trees.

Comparison of phylogenetic placements to pairwise alignments for taxonomic assignment of ciliate OTUs

This study compares taxonomic assignments of ciliate OTUs using pairwise alignment and phylogenetic placement methods, showing differences when OTUs have low similarity to reference databases.

Phylogenetic analysis of SARS-CoV-2 data is difficult

The paper reviews challenges in inferring reliable SARS-CoV-2 phylogenies due to high sequence similarity and low mutation rates, highlighting difficulties in rooting and classification.

Modelling structural constraints on protein evolution via side-chain conformational states

The paper develops a structurally-aware substitution model for amino acid sequence evolution by incorporating side-chain conformational states, showing improved performance in divergence time estimation and tree inference.

Two C++ Libraries for Counting Trees on a Phylogenetic Terrace

The paper introduces two C++ libraries that efficiently count and enumerate trees on a phylogenetic terrace using the SUPERB algorithm, outperforming a Python implementation.

Quartet-based computations of internode certainty provide accurate and robust measures of phylogenetic incongruence

The paper introduces quartet-based measures to quantify phylogenetic incongruence, showing they are more accurate and robust than bipartition-based methods, especially with partial trees and missing data.

A Critical Review on the Use of Support Valuesin Tree Viewers and Bioinformatics Toolkits

This paper reviews issues with branch support values in phylogenetic tree viewers and toolkits, finding that 14/20 tools lack user control over node label semantics, leading to potential errors in tree re-rooting.

Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites

The paper investigates protist diversity in Neotropical rainforest soils, finding them hyperdiverse and dominated by parasitic Apicomplexa, which may influence animal diversity.