Aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. mothur builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. Extensive community-supported documentation and support are available through a MediaWiki-based wiki and a discussion forum.
Supplies a set of methods for community ecologists. vegan is an R package which consists in three main parts: (i) ordination methods such as detrended correspondence or redundancy analysis; (ii) features dedicated to the manipulation of distance matrices including ANOSIM and Mantel tests; and (iii) several utilities to uniformize data as well as a module allowing users to read Cornell Ecology Program file format.
Allows users to perform interactive microbiome analysis. Phyloseq records the complete user input and subsequent graphical results of a user’s session, permitting researchers to archive, share and reproduce the sequence of steps that created their result. This program includes a network panel that animates vertex connectedness as a change in the distance threshold, and scales edge thickness according to inverse distance value.
Phylocom integration, community analyses, null-models, traits and evolution. A software package that provides a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities. The package calculates phylogenetic diversity metrics, performs trait comparative analyses, manipulates phenotypic and phylogenetic data, and performs tests for phylogenetic signal in trait distributions, community structure and species interactions.
Brings together many aspects of today’s cutting-edge genomic, metagenomic, and metatranscriptomic analysis practices to address a wide array of needs. Anvi’o is an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. It empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.
A series of bioinformatics tools for high-throughput sequencing analysis, including pre-processing, clustering, database matching, and classification. With PANGEA, sequences obtained directly from the sequencer can be processed quickly to provide the files needed for sequence identification by BLAST and for comparison of microbial communities.