GALAXY:

• usegalaxy.org.au: has many things but is not specialised

GENE, GENOME COMPARISON and ANNOTATION

• BV-BRC: combines the data and tools from the Legacy BRC resources: PATRIC, the bacterial BRC, and IRD and ViPR, the viral BRCs
• mummer alignments: Galaxy or Mummer homepage
• GenSkew: cumulative GC-skew plots
• GeCoViz: Genomic Context Visualiser

MICROBIAL GROWTH

• QurvE:  software for analyzing time-resolved biological data (growth curves)

MEMBRANE TOPOLOGY, SIGNAL SEQUENCES, ETC.

• DeepTMHMM: A Deep Learning Model for Transmembrane Topology Prediction and Classification

PLASMIDS

• pLannotate: annotate engineered plasmids (bacteria)

PROTEIN STRUCTURE

• PLIP: Protein-Ligand Interaction Profiler

SEARCH ENGINES.

• Fold Seek: protein structure search using pdb file input
• Paper Blast: Find papers published about a gene or protein. “links 735,994 different protein sequences to 1,196,367 scientific article.
• Sites Blast: Given a protein sequence, SitesBLAST finds homologs that have known functional residues and shows whether the functional residues are conserved.

TREES and PHYLOGENY

• iToL (interactive tree of life): online tool for the display, annotation and management of phylogenetic and other trees.
• AnnoTree: for visualization of genome annotations across large phylogenetic trees.

VIRUS GENES, VIRUS DEFENCE GENES and ANNOTATIONS

• Clinker: a pipeline for easily generating publication-quality gene cluster comparison figures
• CRISPR: crispr-Cas++, crisprDetect, AntiCrisprProtein
• PADLOC: The Prokaryotic Antiviral Defence LOCator
• Phastest: PHAge Search Tool with Enhanced Sequence Translation.
• Phynteny: Synteny-based annotation of bacteriophage genes (but only good for bacterial viruses)
• VirFam: identifies head-neck-tail modules and recombinase genes in phage genomes.