Siavash Mirarab

DecoDiPhy deconvolves phylogenetic distance mixtures to improve interpretability and downstream analysis in metagenomics.

BROOQS resolves level-1 phylogenetic networks by efficiently aggregating quartet information without quartet symmetry tests, improving accuracy and scalability.

ROADIES-XP enables efficient incremental species tree updates from raw genomic assemblies using GPU acceleration, achieving high speedups and maintaining topological accuracy.

Phlag detects genomic regions with inconsistent evolutionary processes by modeling gene trees as a stochastic process along the genome.

DipSkmer improves population genomics by accurately estimating genetic diversity in diploid organisms using low-coverage genome skims, outperforming existing methods.

The paper uses whole-genome phylogenomic and synteny data to resolve the evolutionary origin of flatfish body asymmetry, finding strong support for a single origin.

The paper uses genomic data to determine whether flatfish asymmetry evolved once or multiple times, finding strong support for a single origin.

This paper introduces a scalable pipeline for dating species trees that improves accuracy and scalability by addressing gene tree discordance in multi-locus datasets.

SPrUCE estimates genetic diversity from UCE data by correcting underestimation bias using a Gompertz function model, providing accurate results comparable to whole-genome methods.

This paper introduces a method to match branch lengths between trees, improving accuracy in phylogenomic analyses by addressing the challenges of heterogeneous branch length measurements.

The paper introduces krepp, a k-mer-based method for phylogenetic placement of reads on large reference phylogenies, showing improved scalability and accuracy compared to alignment-based methods.

This study reconstructs a time-calibrated hummingbird phylogeny, finding stepwise diversification in the Andes rather than a monophyletic Andean clade.

This paper introduces CASTLES-Pro, a method for estimating species tree branch lengths that accounts for gene duplication, loss, and incomplete lineage sorting, showing improved accuracy over existing methods.

ROADIES infers species trees from raw genome assemblies quickly and accurately, outperforming existing methods in speed while maintaining comparable quality.

This paper introduces KRANK, a k-mer selection algorithm that reduces memory usage while maintaining classification accuracy in taxonomic profiling.

The paper introduces MD-Cat, a method for phylogenetic dating using a categorical rate model, showing improved accuracy over existing methods on datasets with nonmodal or multimodal rate distributions.

CONSULT-II improves taxonomic classification and profiling by combining locality-sensitive hashing with heuristics, achieving higher accuracy for novel species.

This paper introduces C-DEPP, a method that scales deep phylogenetic embedding to large reference trees by using an ensemble approach, enabling efficient placement of 20 million 16S fragments on the GG2 tree in 41 hours.

Greengenes2 aligns 16S rRNA and shotgun metagenomic data using a whole-genome phylogeny, showing agreement in principal coordinates, taxonomy, and phenotype effect size.

DEPP extends species trees using single genes by learning to place them without pre-specified models, enabling integration of 16S and metagenomic data.

The paper evaluates syntenic block detection methods and their impact on rearrangement phylogeny using Mycobacterium tuberculosis genomes, finding that method choice affects results, especially in low-support branches.

The paper introduces an alignment-free method for phylogenetic distance estimation under a no-strand bias model, showing high accuracy in simulations and real data.

RESPECT estimates genome length and repeat spectra from low-coverage genome skims with <1.5% error, outperforming previous methods.

This paper introduces APPLES-2, a distance-based phylogenetic placement method that is more accurate and scalable than existing methods, enabling efficient placement of microbial genomes on large trees.

TAPER identifies and removes small stretches of error in sequence alignments while preserving most of the data, improving alignment accuracy.

CONSULT improves contamination detection in sequencing reads using locality-sensitive hashing, outperforming existing methods and enhancing mitochondrial assembly from genome skims.

This paper introduces ProACT, a phylogenetic method for prioritizing HIV-positive individuals based on viral sequence branch lengths to improve public health resource allocation.

SODA is a species delimitation method that scales to large datasets while maintaining accuracy by using quartet frequencies and testing zero branch lengths in species trees.

This paper introduces a method to improve phylogeny dating by minimizing the variance of log-transformed rate multipliers, showing better accuracy and robustness than existing methods.

ASTRAL-Pro improves species tree inference by handling gene duplication and loss, outperforming existing methods in complex scenarios.