**PHASTER** (PHAge Search Tool Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. http://phaster.ca/ **PhiSpy** is a computer program written in C++, Python and R to identify prophages in a complete bacterial genome sequences. https://github.com/linsalrob/PhiSpy **VirSorter**: mining viral signal from microbial genomic data article https://peerj.com/articles/985/ https://github.com/simroux/VirSorter **VirFinde**r: R package for identifying viral sequences from metagenomic data using sequence signatures https://github.com/jessieren/VirFinder **VirusSeeker** is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin. https://wupathlabs.wustl.edu/virusseeker/ Sequence-based Ultra-Rapid Pathogen Identification **SURPI™** is a computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data generated from clinical samples. http://chiulab.ucsf.edu/surpi/ **Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data** https://www.nature.com/articles/nprot.2017.063