Genomics and Phylogenetic Studies

REFinder improves enzyme discovery from metagenomes by combining alignment-free annotation with targeted assembly, identifying more novel enzymes at lower cost than traditional methods.

RASTRO improves unitig graph path selection by using sequence-based models to identify read-supported branching points in HIV-1 and SARS-CoV-2 assemblies.

alamem and alasight are tools for fast and memory-efficient local alignment and horizontal gene transfer detection in bacterial genomes.

KENT enables fast metagenomic pathogen screening on low-memory hardware using NVIDIA Jetson Nano clusters, achieving speedups while maintaining accuracy comparable to desktop-based methods.

CRAIC provides tools to inspect and curate multiple sequence alignment uncertainty using posterior probabilities from pair-HMM models.

The paper analyzes metaparalog diversity in an Arctic Pelagibacterales population, showing high diversity within a single population and highlighting the importance of pangenome studies for microbiology.

This study uses posterior simulation-based calibration to assess phylogenetic dating methods in BEAST 2, finding good calibration but limited precision in node age estimates.

The paper expands plasmid diversity by analyzing long-read metagenomes, identifying novel plasmid lineages and providing tools for plasmid discovery.

The paper uses conserved synteny analysis to reveal a shared saccharolytic lifestyle across Kiritimatiellia genomes.

D-plus improves introgression detection by addressing rate heterogeneity and ghost lineages, re-analyzing Jaltomata data to challenge prior interpretations.

The paper uses shotgun metagenomic host reads to detect mitochondrial heteroplasmy at allele fractions ≥5% in human respiratory tract samples.

Meta2Data automates retrieval, standardization, and processing of microbiome sequencing data from public repositories for downstream analysis.

MetagenomicsBench evaluates AI agents' ability to analyze metagenomic data through 100 verifiable tasks, finding that performance varies across domains and that technical plausibility does not guarantee correct biological interpretation.

SCiMS predicts host chromosomal sex from metagenomic data, outperforming existing tools at low host coverage and across species.

The paper shows sampling bias in prokaryotic genome collections distorts diversity estimates and proposes a method to detect and reduce this bias.

This paper examines the limits of Bayesian divergence time estimates in microbial evolution, finding that uncertainty scales with distance to calibration points rather than absolute age.

The paper presents a chromosome-level genome assembly for the Eurasian great grey owl, improving resolution of sex chromosomes and microchromosomes compared to previous assemblies.

The paper presents the complete mitochondrial genome of Euterpe precatoria, assembled using PacBio HiFi sequencing and manual curation, revealing structural complexity and gene features characteristic of palm mitochondrial genomes.

The paper develops a generalized maternal-paternal genotype Markov model for diploid DNA, exploring its mathematical formulations and comparing it to existing unphased models.

The paper introduces GrAnnoT and GrAPEx to fully annotate pangenome graphs, integrating annotations from multiple genomes and annotating non-annotated regions, reducing reference bias.

The paper analyzes the Thermococcales pangenome to identify new genera and reveal modular evolution through horizontal gene transfer.

LOAM is a family of genomic language models trained on long-read soil metagenomes, showing competitive performance despite a small training corpus and highlighting the importance of model scale and training data composition.

PhyloZoo provides a Python framework for phylogenetic network analysis, supporting multiple representations and offering tools for visualization and I/O.

This study benchmarks USCOs for phylogenomics, finding that paralogs are common in BUSCO gene sets and can affect phylogenetic accuracy.

Extended Tiberius models outscore Helixer and ANNEVO on all 33 genomes from the five clades all three tools cover, and approach BRAKER3 accuracy in four clades without extrinsic evidence.

The paper optimizes genome assembly and variant discovery for Dermacentor reticulatus ticks using Oxford Nanopore sequencing, identifying workflow parameters that yield high-quality assemblies and genetic insights.

EXCON automates CAFE-based gene family expansion and contraction analysis, identifying 358 rapidly evolving families in primates, including DUX gene copy-number turnover.

FAMUS improves protein annotation by using contrastive learning to compare query sequences against multiple profiles, outperforming existing tools in KEGG and PANTHER annotations.

This paper introduces KRegCCD, a new Bayesian phylogenetic model that improves posterior tree estimation and enables topology testing by providing full support over tree space.

DensiTree 3 is an interactive tool for comparing pairs of tree sets, providing visualizations and CCDs to assess differences in tree distributions and clade support.