- [UPARSE] - [C++/C, v12.0-beta1, 2024.6] - [2013.8, Nat Methods] - [UPARSE: Highly accurate OTU sequences from microbial amplicon reads.]
- [Mothur] - [C++, v1.48.1, 2024.5] - [2009.12, Appl Environ Microbiol] - [Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities.]
- [dada2] - [R, 1.26, 2022.11] - [2016.05, Nat Methods] [DADA2: High resolution sample inference from Illumina amplicon data.]
- [QIIME2] - [JAVA, 2024-05, 2024.05] - [2019.07, Nat Biotechnol] - [Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.]
- [RDP Classifier] - [Java, 2.14, 2023.08] - [2024.03, Microb Ecol] - [Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification.]
- [Tax4Fun] - [R, v0.3.1, 不再更新了] - [2015.05, Bioinformatics] - Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data
- [Tax4Fun2] - [链接无效了] - [2020.05, Environ Microbiome] - [Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences]
- [PICRUSt] - [Python, v1.1.4, 2019.06] - [2013.08, Nat Biotechnol] - [Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.]
- [PICRUSt2] - [Python, v2.5.3, 2024.08] - [2020.06, Nat Biotechnol] - [PICRUSt2 for prediction of metagenome functions.]
- [graftM] - [Python, v0.14.0, 2022.5] - [2018.6, Nucleic Acids Res] - [GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes.]
- [EUKARYOME] - [18S/ITS/28S, v1.9.2, 2024.08] - [2024.06, Database] - [EUKARYOME: the rRNA gene reference database for identification of all eukaryotes.]
- [Silva] - [16S, v138.2, 2024.07] - [2013.1, Nucleic Acids Res] - [The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.]
- [Greengenes2] - [16S, v2022.10, 2022.10] - [2023.07, Nat Biotechnol] - [Greengenes2 unifies microbial data in a single reference tree.]
- [MiDAS] - [16S, v5, 2024.07] - [2024.06, Nat Commun] - [MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters.]