David Emms

A multispecies foundation model for genome function prediction, gene annotation and sequence design

NTv3 is a foundation model that predicts genome function, annotates genes, and designs DNA sequences across species, outperforming existing models in multiple tasks.

Annotating the genome at single-nucleotide resolution with DNA foundation models

The paper introduces SegmentNT, a DNA foundation model for genome annotation, achieving state-of-the-art performance in identifying 14 genic and regulatory elements across species.

OrthoFinder: scalable phylogenetic orthology inference for comparative genomics

OrthoFinder v3 splits orthogroups at duplications predating the species-tree root, raising OrthoBench accuracy, and assigns extra species to a core run, finishing 1024 species in 128 hours.

GENESPACE: syntenic pan-genome annotations for eukaryotes

GENESPACE provides pan-genome annotations to analyze syntenic relationships across diverse eukaryotic genomes, revealing structural variation at multiple biological scales.

SHOOT: phylogenetic gene search and ortholog inference

SHOOT is a tool that places query sequences into phylogenetic trees and identifies orthologs, performing as fast as BLAST and as accurately as conventional tree inference.

Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench

The paper revisits the Orthobench benchmark to assess orthogroup inference methods using updated phylogenetic analyses and provides an open-source benchmarking suite.

OrthoFinder: phylogenetic orthology inference for comparative genomics

OrthoFinder now infers orthogroups, rooted gene and species trees, duplications and orthologs from proteomes alone, topping Quest for Orthologs accuracy tests while rivaling heuristic tools' speed.

STAG: Species Tree Inference from All Genes

STAG is a method for species tree inference that uses multi-copy gene families, showing higher accuracy and scalability compared to existing methods.