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References from A fast comparative genome browser for diverse bacteria and archaea. Local targets link to admitted publications; unresolved targets remain external evidence.
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
10.1038/nbt.4229 · 2018 · External reference
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
10.1038/nbt.3893 · 2017 · External reference
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
10.1101/gr.186072.114 · 2015 · External reference
Conservation of gene order: a fingerprint of proteins that physically interact
10.1016/s0968-0004(98)01274-2 · 1998 · External reference
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context
10.1101/gr.161901 · 2001 · External reference
Predicting protein function by genomic context: quantitative evaluation and qualitative inferences
10.1101/gr.10.8.1204 · 2000 · External reference
Assigning protein functions by comparative genome analysis: protein phylogenetic profiles
10.1073/pnas.96.8.4285 · 1999 · External reference
Lateral gene transfer
10.1016/j.cub.2011.01.045 · 2011 · External reference
Four families of folate-independent methionine synthases
10.1371/journal.pgen.1009342 · 2021 · External reference
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
10.1093/nar/25.17.3389 · 1997 · External reference
Pfam: the protein families database
10.1093/nar/gkt1223 · 2014 · External reference
Tigrfams and genome properties in 2013
10.1093/nar/gks1234 · 2013 · External reference
eggNOG 6.0: enabling comparative genomics across 12 535 organisms
10.1093/nar/gkac1022 · 2023 · External reference
GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective
10.1093/nar/gkac367 · 2022 · External reference
AnnoTree: visualization and exploration of a functionally annotated microbial tree of life
10.1093/nar/gkz246 · 2019 · External reference
PhyloCorrelate: inferring bacterial gene-gene functional associations through large-scale phylogenetic profiling
10.1093/bioinformatics/btaa1105 · 2021 · External reference
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
10.1038/nbt.3988 · 2017 · External reference
GUNC: detection of chimerism and contamination in prokaryotic genomes
10.1186/s13059-021-02393-0 · 2021 · External reference
Curated BLAST for genomes
10.1128/msystems.00072-19 · 2019 · External reference
New finite-size correction for local alignment score distributions
10.1186/1756-0500-5-286 · 2012 · External reference
From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria
10.1371/journal.pbio.0000019 · 2003 · External reference
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
10.1093/molbev/msab293 · 2021 · External reference
Expanded microbial genome coverage and improved protein family annotation in the COG database
10.1093/nar/gku1223 · 2015 · External reference
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
10.1093/bioinformatics/btl158 · 2006 · External reference
CD-HIT: accelerated for clustering the next-generation sequencing data
10.1093/bioinformatics/bts565 · 2012 · External reference
Adaptive seeds tame genomic sequence comparison
10.1101/gr.113985.110 · 2011 · External reference
MUSCLE: multiple sequence alignment with high accuracy and high throughput
10.1093/nar/gkh340 · 2004 · External reference
FastTree 2—approximately maximum-likelihood trees for large alignments
10.1371/journal.pone.0009490 · 2010 · External reference
MicrobesOnline: an integrated portal for comparative and functional genomics
10.1093/nar/gkp919 · 2010 · External reference
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process
10.1186/1471-2105-12-434 · 2011 · External reference
CDD: NCBI’s conserved domain database
10.1093/nar/gku1221 · 2015 · External reference
SANSparallel: interactive homology search against Uniprot
10.1093/nar/gkv317 · 2015 · External reference
InterPro in 2017-beyond protein family and domain annotations
10.1093/nar/gkw1107 · 2017 · External reference
HMMER web server: 2018 update
10.1093/nar/gky448 · 2018 · External reference
Many Families of Lids for TonB-dependent Transporters in Bacteroides
2023 · External reference
STRING 7—recent developments in the integration and prediction of protein interactions
10.1093/nar/gkl825 · 2007 · External reference
The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest
10.1093/nar/gkac1000 · 2023 · External reference
Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighborhood information for protein families
2023 · External reference
FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation
10.1093/bioinformatics/btaa788 · 2021 · External reference
EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools
10.1016/j.jmb.2023.168018 · 2023 · External reference
The IMG/M data management and analysis system v.7: content updates and new features
10.1093/nar/gkac976 · 2023 · External reference
Inference and analysis of the relative stability of bacterial chromosomes
10.1093/molbev/msj052 · 2006 · External reference
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes
10.1093/nar/gkac1078 · 2023 · External reference
The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions
10.1093/bioinformatics/bti070 · 2005 · External reference
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
10.1093/nar/gkab1061 · 2022 · External reference
A powerful non-homology method for the prediction of operons in prokaryotes
10.1093/bioinformatics/18.suppl_1.s329 · 2002 · External reference
A novel method for accurate operon predictions in all sequenced prokaryotes
10.1093/nar/gki232 · 2005 · External reference
