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References from PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN. Local targets link to admitted publications; unresolved targets remain external evidence.
NCBI RefSeq: reference sequence standards through 25 years of curation and annotation
10.1093/nar/gkae1038 · 2025 · External reference
GenBank 2025 update
10.1093/nar/gkae1114 · 2025 · External reference
The IMG/M data management and analysis system v.7: content updates and new features
10.1093/nar/gkac976 · 2023 · External reference
BV-BRC: a unified bacterial and viral bioinformatics resource with expanded functionality and AI integration
10.1093/nar/gkaf1254 · 2026 · External reference
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis
10.1093/nar/gkz926 · 2020 · External reference
AllTheBacteria—all bacterial genomes assembled, available and searchable
10.1101/2024.03.08.584059 · 2024 · External reference
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes
10.1093/nar/gkaf1208 · 2025 · External reference
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”
10.1073/pnas.0506758102 · 2005 · External reference
Roary: rapid large-scale prokaryote pan genome analysis
10.1093/bioinformatics/btv421 · 2015 · External reference
Producing polished prokaryotic pangenomes with the Panaroo pipeline
10.1186/s13059-020-02090-4 · 2020 · External reference
PanACoTA: a modular tool for massive microbial comparative genomics
10.1093/nargab/lqaa106 · 2021 · External reference
PanTools: representation, storage and exploration of pan-genomic data
10.1093/bioinformatics/btw455 · 2016 · External reference
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph
10.1371/journal.pcbi.1007732 · 2020 · External reference
PPanGGOLiN V2: technical enhancement and extended functionalities for prokaryotic pangenome analysis
10.48550/arxiv.2607.24111 · 2026 · External reference
panRGP: a pangenome-based method to predict genomic islands and explore their diversity
10.1093/bioinformatics/btaa792 · 2020 · External reference
panModule: detecting conserved modules in the variable regions of a pangenome graph
10.1101/2021.12.06.471380 · 2021 · External reference
PanExplorer: a web-based tool for exploratory analysis and visualization of bacterial pan-genomes
10.1093/bioinformatics/btac504 · 2022 · External reference
An optimized and integrated robust tool for pangenome generation
10.1007/s10142-026-01847-7 · 2026 · External reference
panX: pan-genome analysis and exploration
10.1093/nar/gkx977 · 2018 · External reference
ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics
10.1093/nar/gkac832 · 2023 · External reference
PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining
10.1093/nar/gkae1042 · 2025 · External reference
EDGAR 3.0: comparative genomics and phylogenomics on a scalable infrastructure
10.1093/nar/gkab341 · 2021 · External reference
MBGD: Microbial Genome Database for Comparative Analysis featuring enhanced functionality to characterize gene and genome functions through large-scale orthology analysis
10.1016/j.jmb.2025.168957 · 2025 · External reference
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
10.1093/nar/gkaf1040 · 2026 · External reference
Nextflow enables reproducible computational workflows
10.1038/nbt.3820 · 2017 · External reference
Empowering bioinformatics communities with Nextflow and nf-core
10.1186/s13059-025-03673-9 · 2025 · External reference
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
10.1101/gr.186072.114 · 2015 · External reference
CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
10.1038/s41592-023-01940-w · 2023 · External reference
Fast and robust metagenomic sequence comparison through sparse chaining with skani
10.1038/s41592-023-02018-3 · 2023 · External reference
Mash: fast genome and metagenome distance estimation using MinHash
10.1186/s13059-016-0997-x · 2016 · External reference
QuickTree: building huge neighbour-joining trees of protein sequences
10.1093/bioinformatics/18.11.1546 · 2002 · External reference
Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets
10.1038/s41597-024-03571-y · 2024 · External reference
CGView.js: a JavaScript package for visualizing small genomes
10.21105/joss.09930 · 2026 · External reference
AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence
10.1038/s41598-021-91456-0 · 2021 · External reference
Acinetobacter baumannii antibiotic resistance mechanisms
10.3390/pathogens10030373 · 2021 · External reference
Comparative genomics of multidrug resistance in Acinetobacter baumannii
10.1371/journal.pgen.0020007 · 2006 · External reference
Comparative analysis of AbaR-type genomic islands reveals distinct patterns of genetic features in elements with different backbones
10.1128/msphere.00349-20 · 2020 · External reference
Genomics unveils country-to-country transmission between animal hospitals of a multidrug-resistant and sequence type 2 Acinetobacter baumannii clone
10.1099/mgen.0.001292 · 2024 · External reference
Panorama: a robust pangenome-based method for predicting and comparing biological systems across species
10.1371/journal.pcbi.1013856 · 2026 · External reference