A review of software for analyzing molecular sequences

Background Over the past ten years, there has been an explosion of microbiome research. Many software packages for analyzing microbial sequences such as the 16S gene from 454 sequencers and Illumina platforms are available. But for a new researcher, it is difficult to know which package to choose. We present a systematic review of packages for the analysis of molecular sequences used to describe and compare microbial communities. This review gives students and researchers information to help choose the best analytic pipeline for their project. To the best of our knowledge, this is the first review of such software. Findings Seven software packages met our inclusion criteria of being cost free and publically available, offering analysis functions from platform sequencing to results presentation, and included documentation and data security. We installed and executed each of the software packages and describe the installation, documentation, features, and functions of each. Conclusions For the user, pipeline choices may be limited because some packages only run on select operating systems. Users should be aware of the availability of features and functions of each package. Of utmost importance is that the user must be aware of the default settings and underlying assumptions of each function. All packages are lacking sufficient methods for longitudinal analysis. Researchers can do well using any one of these seven packages. However, two packages are outstanding; mothur and QIIME, due not only to the comprehensive suite of functions and procedures incorporated into the pipelines but also because of the accompanying documentation