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Farid MUSA
Farid MUSA

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Software and Tools for Amplicon Metagenomics


    • Description: Nice and clean web application for visualizing phylogenetic trees.
    • Link:
  2. MicrobiomeAnalyst

Software and Tools

  1. QIIME2
  2. mothur
    • 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:
    • 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:
  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:
  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:
  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:
  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:

R packages

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

Top comments (0)

Regex for lazy developers

regex for lazy devs

You know who you are. Sorry for the callout 😆