B. Q. Minh

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

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

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.

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

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.

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

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

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

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

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

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

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.