Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)

Area of Science:

• Molecular evolution
• Bioinformatics
• Computational biology

Background:

• Heterochronous (temporally sampled) gene sequence data are crucial for molecular phylogenetics on timescales of months to years.
• Such data are increasingly vital in fields like molecular epidemiology, especially for rapidly evolving viruses.

Purpose of the Study:

• Introduce TempEst, a cross-platform software for visualizing and analyzing temporally sampled sequence data.
• Provide a tool to assess the suitability of data for molecular clock phylogenetic analysis.
• Identify potential data quality issues in sequence datasets.

Main Methods:

• Utilizes an interactive regression approach to analyze the relationship between genetic divergence and sampling dates.
• Input requires a molecular phylogeny and the sampling dates for each sequence.
• Facilitates exploration of temporal signal within sequence datasets.

Main Results:

• TempEst enables users to evaluate the sufficiency of temporal signal for molecular clock analyses.
• The software can detect incongruent sequences, highlighting potential errors in data annotation, contamination, recombination, or alignment.
• Identifies sequences that deviate significantly from expected evolutionary trajectories based on sampling time.

Conclusions:

• TempEst is a valuable tool for researchers using molecular clock models, particularly those implemented in BEAST.
• Recommends pre-analysis data checking with TempEst to ensure data quality and reliability.
• Enhances the accuracy and robustness of phylogenetic reconstructions from heterochronous sequence data.