Bùi Quang Minh

DGM Is Dead; Long Live DGM-Star! A Quantization-Theoretic Approach to Gamma Rate Discretization

The paper introduces a new method to discretize Gamma rate distributions in phylogenetics, reducing branch length bias compared to the standard DGM.

A New Information Theoretic Approach Shows that Mixture Models Outperform Partition Models for Phylogenetic Analyses of Amino Acid Data

The paper compares mixture and partition models for phylogenetic analyses using the mAIC and finds mixture models consistently outperform partition models.

PartitionFinder-mAIC: Phylogenetic Partitioning using Marginal Akaike Information Criterion

PartitionFinder-mAIC improves phylogenetic partitioning by using marginal AIC, resulting in fewer partitions and better inference of green plant evolution.

ProtFinder: An efficient machine learning framework for protein model selection on real data

ProtFinder is a machine learning framework for protein model selection that outperforms existing methods in accuracy and speed on real datasets.

Modeling Site-Specific Mutation Patterns in Pandemic-Scale Phylogenetics

This paper introduces a site-specific mutation model (SSM) for pandemic-scale phylogenetics, showing it better captures mutation patterns in SARS-CoV-2 genomes than classical models.

Tryptophan became part of the universal genetic code post-LUCA

The paper investigates whether tryptophan was present in LUCA by analyzing the evolution of tryptophanyl-tRNA synthetase and finds that W usage originated in Bacteria with later horizontal transfer to Archaea.

GTRspmix: Capturing Heterogeneity of Exchangeabilities Across Sites to Improve Protein Phylogenetics

GTRspmix improves protein phylogenetics by incorporating multiple exchangeability matrices into mixture models, enhancing fit and reducing long-branch attraction artifacts.

CMAPLE 2: Fast and Accurate Phylogenetic Inference for Millions of Pathogen Genomes

CMAPLE 2 improves phylogenetic inference speed and memory efficiency for large pathogen genome datasets, enabling analysis of nearly four million SARS-CoV-2 genomes in 12 days.

piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE

piqtree provides a Python interface to IQ-TREE for phylogenetic inference, offering seamless integration with Python tools and workflows.

Rate variation and recurrent sequence errors in pandemic-scale phylogenetics

The paper improves pandemic-scale phylogenetic analysis by addressing mutation rate variation and sequence errors, reconstructing a reliable phylogenetic tree of over 2 million SARS-CoV-2 genomes.

Robust Phylogenetics

This paper introduces a robust phylogenetic inference method that dynamically identifies and removes problematic sites in sequence alignments, outperforming existing methods while being implemented in IQ-TREE2.

A robustly rooted tree of eukaryotes reveals their excavate ancestry.

This study estimates the root of the eukaryote Tree of Life using mitochondrial proteins, finding it between Opimoda+ and Diphoda+ supergroups.

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.

TreeFormer: A transformer-based tree rearrangement operation for phylogenetic reconstruction

TreeFormer improves phylogenetic tree reconstruction accuracy using a transformer-based tree rearrangement method, outperforming FastTree 2 on small alignments.

This is SPRTA: assessing phylogenetic confidence at pandemic scales

SPRTA assesses phylogenetic confidence by evaluating evolutionary histories rather than clades, applied to a global SARS-CoV-2 dataset.

GTRpmix: A linked general-time reversible model for profile mixture models

The paper introduces GTRpmix, a model for profile mixture models that improves exchangeability matrix estimation for site-heterogeneous data, enhancing phylogenetic accuracy.

CMAPLE: efficient phylogenetic inference in the pandemic era

The paper introduces CMAPLE, an optimized phylogenetic inference method, and integrates it into IQ-TREE 2 for improved pandemic-scale genomic analysis.

MAST: Phylogenetic Inference with Mixtures Across Sites and Trees

The paper introduces the MAST model for phylogenetic inference using concatenated alignments with multiple evolutionary histories, showing it can accurately recover tree parameters and detect incomplete lineage sorting and introgression.

Maximum likelihood pandemic-scale phylogenetics

The paper introduces MAPLE, a new phylogenetic analysis method that scales to large datasets by improving computational efficiency, outperforming existing tools like FastTree and RAxML-NG.

Updated site concordance factors minimize effects of homoplasy and taxon sampling

The paper introduces an updated site concordance factor method that reduces homoplasy and taxon sampling effects using likelihood-based ancestral state probabilities.

AliSim: A Fast and Versatile Phylogenetic Sequence Simulator For the Genomic Era

AliSim efficiently simulates biologically realistic alignments under complex evolutionary models, outperforming existing tools in speed and resource usage.

nQMaker: estimating time non-reversible amino acid substitution models

nQMaker estimates time non-reversible amino acid substitution models and rooted phylogenetic trees from protein sequence alignments, showing improved model fit across diverse datasets.

A comprehensive phylogenetic analysis of the serpin superfamily

This study constructs a comprehensive phylogeny of 6000 serpin sequences across all kingdoms of life, showing convergent evolution rather than horizontal gene transfer for the central hub proteins.

New methods to calculate concordance factors for phylogenomic datasets

IQ-TREE 2 implements taxon-coverage-aware gene concordance factors and introduces site concordance factors, quantifying gene- and site-level discordance that 100% bootstrap support leaves hidden.

The Prevalence and Impact of Model Violations in Phylogenetics

Permutation-based maximal matched-pairs symmetry tests show 40.8% of 3,572 partitions from 35 published phylogenetic datasets reject stationary, reversible, homogeneous evolution, frequently altering inferred tree topologies.

Polymorphism-aware species trees with advanced mutation models, bootstrap and rate heterogeneity

This paper introduces PoMo, a polymorphism-aware phylogenetic model that improves species tree inference by accounting for polymorphisms and integrates advanced mutation models and rate heterogeneity.