Software and Tools for Amplicon Metagenomics


WebApps/WebTools


  1. Phylo.io
    • Description: Nice and clean web application for visualizing phylogenetic trees.
    • Link: http://phylo.io/
  2. MicrobiomeAnalyst

Software and Tools


  1. QIIME2
  2. mothur
  3. KRAKEN
  4. USEARCH
    • Description: USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
    • Link: https://www.drive5.com/usearch
  5. VSEARCH
    • Description: VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool.
    • Link: https://github.com/torognes/vsearch
  6. MG-RAST
    • Description: MG-RAST is an open source, open submission web application server that suggests automatic phylogenetic and functional analysis of metagenomes.
    • Link: https://www.mg-rast.org
  7. PICRUSt
    • Description: PICRUSt (pronounced “pie crust”) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.
    • Link: http://picrust.github.io/picrust
  8. pplacer
    • Description: Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.
    • Link: https://matsen.fhcrc.org/pplacer
  9. The Exelixis Lab [Curated Collection of Software/Tools]
    • Description: Include software/tools for:
      • Phylogenetic Inference
      • Phylogenetic Post-Analysis
      • Next Generation Sequencing & Sequence Analysis
      • Population genetics
      • Web services
      • etc.
    • Link: https://cme.h-its.org/exelixis/software.html

R packages


  1. microbiome
  2. microbiomeSeq
  3. matR - Metagenomics Analysis Tools
  4. MonoPhy

[microbiome amplicon-metagenomics tools packages software curated-external phylogenetic ]