Robert Lanfear

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

This study evaluates the accuracy of eucalypt taxonomy by comparing gene tree topologies to a concatenated species tree, revealing inconsistencies in taxonomic groupings.

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

PhyloRBT detects reference bias in phylogenomic datasets by comparing locus reconstructions across multiple reference genomes, identifying biased loci that affect species tree inference.

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

PhyloNOW improves phylogenomic analyses by allowing variable window sizes across chromosomes, outperforming fixed-size methods on simulated data and showing size variation in empirical datasets.

The paper introduces a new method to detect and characterize introgression in large species trees by analyzing discordant attachment frequencies of gene trees, demonstrating its application in cichlids and Drosophila.

This study analyzes 63 Megalocytivirus genomes, revealing widespread recombination and identifying genes from outside the Iridoviridae family, leading to the designation of two new species.

This study proposes using AIC to select optimal window sizes for whole genome alignments, finding shorter windows for butterflies and longer for great apes, with varying impacts on topology recovery.

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.

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

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

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.

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

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

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

This study compares online and de novo phylogenetic methods for SARS-CoV-2, finding that maximum parsimony online approaches are more accurate and efficient than maximum likelihood or de novo methods.

The paper introduces UShER, a method for ultrafast phylogenetic placement of SARS-CoV-2 sequences, enabling real-time genomic contact tracing and maintaining an updated reference phylogeny.

The paper estimates changes in SARS-CoV-2 transmissibility using a phylogeny-based metric, finding that Delta is the most transmissible clade and transmissibility within clades slightly decreases over time.

sangeranalyseR provides an interactive R package and Shiny apps for analyzing Sanger sequencing data, offering tools for read trimming, peak detection, and indel analysis.

The paper identifies lab-specific recurrent mutations in SARS-CoV-2 sequences that affect phylogenetic inference and proposes tools to improve sequence quality and phylogeny comparison.

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 paper estimates the somatic mutation rate in a long-lived Eucalyptus tree using a novel method, finding it lower per unit of growth compared to Arabidopsis.

The paper presents a draft genome assembly of Eucalyptus pauciflora using long and short-read data and evaluates four assemblers to identify the best assembly.

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.

The paper evaluates chloroplast genome assembly methods using Eucalyptus pauciflora, finding that hybrid long- and short-read assemblies are most accurate.

The paper presents an open-source workflow for establishing MinION long-read sequencing in any laboratory, achieving >8.5 Gb of data with mean read length 13 kb and N50 26 kb.