B. Q. Minh

MixtureFinder: Estimating DNA mixture models for phylogenetic analyses

MixtureFinder estimates optimal DNA mixture models for phylogenetic analyses by selecting the best number of classes for Q matrices in DNA sequence evolution.

Order of amino acid recruitment into the genetic code resolved by Last Universal Common Ancestor's protein domains

The paper infers the order of amino acid recruitment into the genetic code by analyzing ancestral protein domain frequencies, finding smaller amino acids were added earlier and metal-binding/sulfur-containing amino acids earlier than previously thought.

AliSim-HPC: parallel sequence simulator for phylogenetics

AliSim-HPC accelerates phylogenetic sequence simulation using parallel computing, reducing runtime for large alignments by 162-fold.

DecentTree: Scalable Neighbour-Joining for the Genomic Era

DecentTree improves Neighbour-Joining phylogenetic inference scalability, handling large datasets up to 64,000 SARS-CoV-2 genomes faster than existing methods.

The Influence of Model Violation on Phylogenetic Inference: A Simulation Study

This study simulates datasets with varying degrees of non-SRH conditions to assess the impact of SRH model violations on phylogenetic inference, finding that maximum likelihood is robust except under extreme convergent evolution.

A test statistic to quantify treelikeness in phylogenetics

This paper introduces a test statistic called tree proportion to quantify treelikeness in phylogenetic alignments and evaluates its performance through simulations.

Are fleas highly modified Mecoptera? Phylogenomic resolution of Antliophora (Insecta: Holometabola)

This study uses transcriptomic data to resolve the phylogenetic relationships within Antliophora, finding fleas are sister to either a monophyletic Mecoptera or arose within mecopteran families, potentially making Mecoptera paraphyletic.

Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Non-Reversible Models for Mammals

This study evaluates non-reversible models for rooting empirical phylogenies and introduces the rootstrap bootstrap measure to assess root placement confidence.

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

This study uses genome-wide data to resolve primate phylogenetic relationships, identifying multiple radiations and ancient introgression events.

Undinarchaeota illuminate the evolution of DPANN archaea

The paper reconstructs genomes of Undinarchaeota, a new DPANN archaeal lineage, and analyzes their phylogenetic placement and potential gene exchange with hosts.

QMaker: Fast and accurate method to estimate empirical models of protein evolution

QMaker estimates empirical amino acid substitution models using ML, improving model fit and phylogenetic inference.

IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era

IQ-TREE 2 introduces new models and efficient methods for phylogenetic inference, improving upon its previous version for genomic data analysis.

GHOST: Recovering Historical Signal from Heterotachously-evolved Sequence Alignments

The paper introduces the GHOST model to improve phylogenetic inference from heterotachously-evolved sequences, showing it accurately recovers tree topologies and provides new insights into historical signals in empirical data.

UFBoot2: Improving the Ultrafast Bootstrap Approximation

UFBoot2 improves the ultrafast bootstrap approximation for phylogenetic analyses by increasing speed and reducing overestimation of branch supports.

Complex models of sequence evolution require accurate estimators as exemplified with the invariable site plus Gamma model

The paper shows that the invariable site plus discrete Gamma model's parameters are poorly estimated by current software and proposes an improved optimization heuristic.