Virome is a web application interface to databases and tools for the analysis of viral metagenome sequence data. The long term aim of the VIROME project is to create a framework for understanding the inﬂuence of viral genes on the evolution and ecology of their hosts.
Real-time metagenomics is a rapid replacement for mg-rast and other slow software. RTMG will analyze your data in minutes, and returns the raw results. Several hundred public metagenomes have been annotated with RTMG and are available in a preprocessed form - or you can download them and rerun them yourself ... it won't take long.
MG-RAST is the de-facto metagenome annotation site. You can upload data and have it annotated and analyzed here. It handles thousands of metagenomes and has over 500 publicly available samples that you can browse without a username.
Megx.net allows access to integrated environmental and (meta)genomic data intended for use in marine microbial ecology. This section of Megx.net lists marine phage genomes.
CAMERA stands for Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis. The aim of this project is to serve the needs of the microbial ecology research community by creating a rich, distinctive data repository and a bioinformatics tools resource that will address many of the unique challenges of metagenomic analysis
SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It comes with built-in support for state-of-the-art software for essential metagenomic tasks such as assembly and gene prediction, and can be easily extended to support additional software. SmashCommunity provides tools to estimate the quantitative phylogenetic and functional compositions of metagenomes, compare compositions of multiple metagenomes and produce intuitive visual representations of such analyses.
IMG/M provides tools for analyzing the functional capability of microbial communities based on their metagenome sequence, in the context of reference isolate genomes included from the Integrated Microbial Genomes (IMG) system. IMG/M contains metagenome data generated from 65 microbial community samples that are part of 20 metagenome studies, out of which 19 are new samples and 6 are new studies.
MEGAN (“MEtaGenome ANalyzer”) is a computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.