- Description: Nice and clean web application for visualizing phylogenetic trees.
- Link: http://phylo.io/
- Description: MicrobiomeAnalyst is a comprehensive statistical, visual and meta-analysis of microbiome data.
- Link: https://www.microbiomeanalyst.ca
- 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
- 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
- Description: Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences.
- Link: http://ccb.jhu.edu/software/kraken
- 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
- 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
- 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
- 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
- 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
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
- Link: https://cme.h-its.org/exelixis/software.html
- 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
- Link: https://github.com/umerijaz/microbiomeSeq
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
- Link: https://rdrr.io/cran/matR
- 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
- Link: https://cran.r-project.org/web/packages/MonoPhy/index.html