Online bacterial genomics data analysis tools

A very non-exhaustive list of online resources for bacterial genomic analysis for those just starting out in pathogen genomics. Please note I am not affiliated with these tools, unless otherwise stated, nor have I explored their full functionality.

Data visualisation

Interactive Tree Of Life (iTOL) is an online tool for the display, annotation and management of phylogenetic and other trees.
URL: https://itol.embl.de/.

Phandango: Interactive visualization of genome phylogenies.
URL: https://jameshadfield.github.io/phandango/#/.

Microreact: Open data visualization and sharing for genomic epidemiology.
URL: https://microreact.org/.

Genetic epidemiology

PathogenWatch: A Global Platform for Genomic Surveillance.
URL: https://pathogen.watch/

AMR

CARD: The Comprehensive Antibiotic Resistance Database.
URL https://card.mcmaster.ca/

Beta-Lactamase Database:.
http://bldb.eu/

ResFinder: ResFinder identifies acquired genes and/or finds chromosomal mutations mediating antimicrobial resistance in total or partial DNA sequence of bacteria.
URL: https://cge.cbs.dtu.dk/services/ResFinder/

Bacteriophages

VIPTree: the Viral Proteomic Tree server.
URL: https://www.genome.jp/viptree/ PHASTER.
https://phaster.ca/
PhageCompass:
URL: http://www.phagecompass.dk/
VIRIDIC:
URL: https://rhea.icbm.uni-oldenburg.de/viridic/

Baceriocines

BAGEL4:
URL: http://bagel4.molgenrug.nl/

Insertion sequences

ISFinder.
URL: https://isfinder.biotoul.fr/

CRISPR

CRISPRCasFinder.
https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index

Transposons

TnCentral.
URL: https://tncentral.proteininformationresource.org/

Plasmids

PlasmidFinder:
URL: https://cge.food.dtu.dk/services/PlasmidFinder/

Plasmid MLST:
URL: https://cge.food.dtu.dk/services/pMLST/

Proteins

The STRING database: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
URL: https://string-db.org/

FoldX: effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. \
https://foldxsuite.crg.eu/node/196

ModWeb: Protein structure modelling.
https://modbase.compbio.ucsf.edu/modweb/

TMHMM - 2.0: Prediction of transmembrane helices in proteins.
URL: https://services.healthtech.dtu.dk/service.php?TMHMM-2.0

InterProScan: Classification of protein families
URL: https://www.ebi.ac.uk/interpro/

Prot pi: a web application for calculating physico-chemical parameters of proteins and peptides.
URL: https://www.protpi.ch/

CELLO2GO: A web server for protein subCELlular LOcalization prediction with functional Gene Ontology annotation.
URL: http://cello.life.nctu.edu.tw/cello2go/

Annotation

RAST: Rapid Annotation using Subsystem Technology.
URL: https://rast.nmpdr.org/

ORF prediction

Glimmer: Microbial gene finding system.
URL: http://ccb.jhu.edu/software/glimmer/index.shtml

ORFinder: Open Reading Frame Finder.
URL: https://www.ncbi.nlm.nih.gov/orffinder/

GeneMarkS:.
URL: http://exon.gatech.edu/genemark/genemarks.cgi

tRNA detection

tRNAscan-SE: Searching for tRNA genes in genomic sequences.
URL: http://lowelab.ucsc.edu/tRNAscan-SE/

ARAGORN: ARAGORN detects tRNA, mtRNA info about tmRNA, and tmRNA genes
URL: http://www.ansikte.se/ARAGORN/

Selection

HyPhy: Selection & dN/dS.
URL: https://www.datamonkey.org/