A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes

Area of Science:

• Microbiology
• Bioinformatics
• Evolutionary Biology

Background:

• Phylogenetic analysis is crucial for microbial taxonomy and identification globally.
• Existing research lacks standardized protocols for data analysis and phylogenetic tree reconstruction.
• This variability hinders comparability and reliability of phylogenetic studies.

Purpose of the Study:

• To provide a user-friendly Standard Operating Procedure for Phylogenetic Inference (SOPPI).
• To standardize the process from field sampling to phylogenetic tree reconstruction and publication.
• To enhance the reliability and comparability of microbial phylogenetic and diversity analyses.

Main Methods:

• The SOPPI focuses on ribosomal RNA as a universal phylogenetic marker.
• Principles can be adapted for any suitable marker gene.
• Guidelines cover the entire workflow: sampling, data analysis, and tree reconstruction.

Main Results:

• The SOPPI offers a practical framework for consistent phylogenetic inference.
• It aims to improve the reproducibility of results between different research laboratories.
• The procedure is designed to be adaptable and inclusive of community feedback.

Conclusions:

• The SOPPI serves as a valuable resource for researchers conducting phylogenetic analyses.
• It promotes standardization, leading to more reliable and comparable scientific outcomes.
• Continuous community input will drive future improvements and updates to the guidelines.