mothur

mothur is a software package used for analyzing high-throughput sequencing data, particularly from microbial communities. It was originally developed for analyzing 16S rRNA gene sequences, a common marker gene used to identify and quantify bacteria and archaea. The software provides a comprehensive pipeline for processing these sequences, from quality control and chimera checking to clustering and diversity analysis.

The mothur workflow typically involves several steps. Raw sequencing reads are first filtered and trimmed to remove low-quality bases and adapter sequences. Then, sequences are aligned to a reference alignment to ensure comparability. Chimeric sequences, which can arise during PCR amplification, are identified and removed. Sequences are then clustered into operational taxonomic units (OTUs) based on sequence similarity, representing different microbial taxa. Finally, mothur allows for various downstream analyses, including estimating alpha diversity (diversity within a sample) and beta diversity (diversity between samples), as well as constructing phylogenetic trees.

Beyond 16S rRNA data, mothur has been adapted for analyzing other types of high-throughput sequencing data, such as ITS (Internal Transcribed Spacer) sequences for fungal communities and metagenomic data. Its open-source nature and extensive documentation have made it a widely adopted tool in microbial ecology and related fields. The software is command-line based, which allows for reproducible and automated analyses.