Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 75 (23), 7537-41

Introducing Mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Affiliations

Introducing Mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Patrick D Schloss et al. Appl Environ Microbiol.

Abstract

mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

Figures

FIG. 1.
FIG. 1.
Description and comparison of the eight samples analyzed by Sogin et al. (27). The dendrogram to the left represents the similarity of the samples based on the membership-based Jaccard coefficient calculated using Chao1 estimated richness values. The dendrogram on the right represents the similarity of the samples based on the structure-based θYC coefficient. The distance from the tip of the dendrogram to the root is 0.50 for both trees.
FIG. 2.
FIG. 2.
Rarefaction curves describing the dependence of discovering novel OTUs as a function of sampling effort for OTUs defined at a 0.10 distance cutoff. The curves for FS312 and FS396 climb to 3,095 and 2,804 OTUs after sampling of 54,894 and 80,769 sequences, respectively.

Similar articles

See all similar articles

Cited by 4,829 PubMed Central articles

See all "Cited by" articles

Publication types

LinkOut - more resources

Feedback