R. Lanfear

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.

Testing for phylogenetic signal in single-cell RNA-seq data

This study shows that scRNA-seq data can be used for phylogenetic analysis, revealing tumor clonal composition through expression levels and SNVs.

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.

matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2

matOptimize improves runtime and memory efficiency for SARS-CoV-2 phylogenetic tree optimization, enabling daily maintenance of large-scale phylogenies during the pandemic.

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.

Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region

The paper develops a novel phylogenomic method to detect recombination events in SARS-CoV-2 genomes, identifying 606 recombination events across 1.6M samples with 2.7% of genomes showing recombinant ancestry, primarily in the Spike protein region.

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.

Mutation rates and selection on synonymous mutations in SARS-CoV-2

The paper analyzes mutation rates and selection pressures in SARS-CoV-2 genomes, identifying elevated G→U and C→U mutations and challenging previous findings on synonymous site selection.

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.

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.

Stable and widespread structural heteroplasmy in chloroplast genomes revealed by a new long-read quantification method

The paper introduces Cp-hap, a method to detect chloroplast structural haplotypes using long-read sequencing, revealing two widespread haplotypes in most land plants.

Linking Branch Lengths Across Loci Provides the Best Fit for Phylogenetic Inference

This study finds that proportionally linking branch lengths across loci provides the best fit for phylogenetic inference compared to other models.