Software and Tools for Amplicon Metagenomics
Tags: curatedexternalsourc, microbiome, ampliconmetagenomics, tools
Published: 2021-04-11 15:45:40

---
title: Software and Tools for Amplicon Metagenomics
published: true
date: 2019-09-03 00:00:00 UTC
tags: CuratedExternalSourc,microbiome,ampliconmetagenomics,tools
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---

## WebApps/WebTools

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1. **Phylo.io**
  - **Description:** Nice and clean web application for visualizing phylogenetic trees.
  - **Link:** [http://phylo.io/](http://phylo.io/)
2. **MicrobiomeAnalyst**
  - **Description:** MicrobiomeAnalyst is a comprehensive statistical, visual and meta-analysis of microbiome data.
  - **Link:** [https://www.microbiomeanalyst.ca](https://www.microbiomeanalyst.ca)

## Software and Tools

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1. **QIIME2**
  - **Description:** QIIME2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.
  - **Link:** [https://docs.qiime2.org/2019.7/install](https://docs.qiime2.org/2019.7/install)
2. **mothur**
  - **Description:** mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data.
  - **Link:** [https://github.com/mothur/mothur/releases/tag/v.1.43.0](https://github.com/mothur/mothur/releases/tag/v.1.43.0)
3. **KRAKEN**
  - **Description:** Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences.
  - **Link:** [http://ccb.jhu.edu/software/kraken](http://ccb.jhu.edu/software/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](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](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](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](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](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](https://cme.h-its.org/exelixis/software.html)

## R packages

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1. **microbiome**
  - **Description:** Tools for the exploration and analysis of microbiome profiling data sets, in particular large-scale population studies and 16S taxonomic profiling.
  - **Tutorial:** [https://microbiome.github.io/tutorials](https://microbiome.github.io/tutorials)
  - **Link:** [https://github.com/microbiome/microbiome](https://github.com/microbiome/microbiome)
2. **microbiomeSeq**
  - **Description:** An R package for microbial community analysis in an environmental context
  - **Tutorial:** [http://userweb.eng.gla.ac.uk/umer.ijaz/projects/microbiomeSeq\_Tutorial.html](http://userweb.eng.gla.ac.uk/umer.ijaz/projects/microbiomeSeq_Tutorial.html)
  - **Link:** [https://github.com/umerijaz/microbiomeSeq](https://github.com/umerijaz/microbiomeSeq)
3. **matR - Metagenomics Analysis Tools**
  - **Description:** An analysis platform for metagenomics combining specialized tools and workflows, easy handling of the BIOM format, and transparent access to MG-RAST resources. Integrates easily with other R packages and non-R software.
  - **Tutorial:** [https://www.mcs.anl.gov/~braithwaite/matR/docs-and-pubs/matR-user-manual.pdf](https://www.mcs.anl.gov/~braithwaite/matR/docs-and-pubs/matR-user-manual.pdf)
  - **Link:** [https://rdrr.io/cran/matR](https://rdrr.io/cran/matR)
4. **MonoPhy**
  - **Description:** The R package MonoPhy allows assessment and exploration of monophyly of taxa in a phylogeny.
  - **Tutorial:** [https://cran.r-project.org/web/packages/MonoPhy/vignettes/MonoPhyVignette.html](https://cran.r-project.org/web/packages/MonoPhy/vignettes/MonoPhyVignette.html)
  - **Link:** [https://cran.r-project.org/web/packages/MonoPhy/index.html](https://cran.r-project.org/web/packages/MonoPhy/index.html)