PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and...

Area of Science:

• Bioinformatics
• Computational Biology
• Evolutionary Biology

Background:

• Multigene and genomic datasets are increasingly common in phylogenetics.
• Existing tools often lead to time-consuming and complex analyses for these large datasets.

Purpose of the Study:

• To present PhyloSuite, a desktop platform designed to streamline molecular sequence data management and phylogenetic analysis.
• To provide a user-friendly workflow for both beginners and experienced researchers.

Main Methods:

• PhyloSuite is a cross-platform, open-source Python graphical user interface (GUI) with a plugin-based system.
• It integrates tools for data acquisition, sequence alignment (mafft, macse), alignment optimization (trimAl, HmmCleaner, Gblocks), dataset concatenation, model selection (PartitionFinder, modelfinder), and phylogenetic inference (MrBayes, iq-tree).
• Features include a drag-and-drop GUI, data management workplace, GenBank extraction, and batch processing capabilities.

Main Results:

• PhyloSuite offers a streamlined workflow from data acquisition to phylogenetic tree annotation (with iTOL).
• The platform simplifies complex analyses, reducing the need for manual file transfer between different software.
• It supports beginners in starting phylogenetic analyses and allows experienced researchers to manage their work efficiently.

Conclusions:

• PhyloSuite enhances the efficiency of molecular data management and phylogenetic analyses.
• The integrated platform allows researchers to focus more on scientific questions rather than software complexities.
• It serves as a valuable tool for advancing evolutionary phylogenetics research.