Table 3.
Available tools for analysis of viruses in total community and viral metagenomes
| Name | Description | Website/reference(s) |
|---|---|---|
| PHACCS89 | Assesses the biodiversity of viromes; requires knowledge of virus genome sizes; desktop app | https://sourceforge.net/projects/phaccs/ |
| ACLAME90 | Classification of mobile genetic elements; web‐based | http://aclame.ulb.ac.be |
| MetaVir 291, 92 | Annotates viral metagenomes (raw reads or assembled contigs); web‐based | http://metavir-meb.univ-bpclermont.fr |
| VIROME93 | Classification of predicted open‐reading frames (ORFs) from viral metagenomes; each ORF placed into one of 9 sequence categories; functional classification; web‐based | http://virome.dbi.udel.edu |
| Vanator94 | Perl pipeline using a number of alignment, assembly and analysis tools to assess metagenomic data derived from Illumina data; virus discovery; desktop app | https://sourceforge.net/projects/vanator-cvr/ |
| VirSorter95 | Detects virus signals in single‐cell amplified genomes of uncultivated organisms or genomic fragments assembled from metagenomic sequencing; desktop app | https://github.com/simroux/VirSorter |
| ViromeScan96 | Characterises taxonomy of eukaryotic viruses directly from raw reads; desktop app | https://sourceforge.net/projects/viromescan/ |
| VIP97 | Identification of eukaryotic viruses (pathogens, influenza virus) from metagenomes; desktop app | https://github.com/keylabivdc/VIP |
| VirusDetect98 | Analyses small RNA datasets for known and novel viruses; web‐based and desktop app | http://bioinfo.bti.cornell.edu/tool/VirusDetect/ |
| PHASTER99 | PHAge Search Tool—Enhanced Release, rapid identification and annotation of prophage sequences within bacterial genomes, plasmids and metagenomic sequences | http://phaster.ca/ |
| VirusSeeker100 | BLAST‐based sequence analysis pipeline for eukaryotic and prokaryotic virus discovery and virome composition; desktop app | https://wupathlabs.wustl.edu/virusseeker/ |
| VirHostMatcher74 | Computes Oligonucleotide Frequency (ONF) scores between viral and host sequences in total community metagenomes, and visualises results; higher predictive accuracy at class and phylum levels | https://github.com/jessieren/VirHostMatcher |
| VirFinder73 | k‐mer frequency‐based, machine‐learning method for virus contig identification in total community metagenomes | https://github.com/jessieren/VirFinder |