Analyzing numerical data validating identification numbers
Metapath Metapath is a statistical package for comparing metagenomic data-sets at the pathway level (using KEGG pathway information).Metapath relies on a graph-theoretic definition of statistical significance in order to identify pathway motifs that differ between samples from two treatment populations.
PRINSEQ A sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data.Microbiome Utilities A set of software utilities for processing and analyzing 16S r RNA genes including generating NAST alignments, chimera checking, and assembling paired 16S r RNA reads according to reference sequence homology Mothur A platform-independent software package for describing and comparing microbial communities.Mothur incorporates the functionality of a number of computational tools, calculators & visualization tools into a single program R-package: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP This R-package provides several functions to perform formal hypothesis testing on the species abundance distribution of human microbiome data, and to calculate power and sample size requirements for human microbiome experiments.Decon Seq is available as both standalone and web-based versions.
DNAclust DNAclust is a fast clustering algorithm specifically designed for high-stringency clustering of DNA sequences, e.g.
Initial HMP walkthroughs utilize Clo VR, a desktop application integrating state-of-the-art genomic tools in a robust, user friendly, fully automated software package with optional support for cloud computing platforms.