EAPhy: A Flexible Tool for High-throughput Quality Filtering of Exon-alignments and Data Processing for Phylogenetic...

Area of Science:

• Evolutionary Biology
• Genomics
• Bioinformatics

Background:

• Molecular methods allow sequencing of thousands of loci for evolutionary studies.
• Visual inspection of alignments is challenging with large genomic datasets.
• The impact of missing data on phylogenetic inference is often under-explored.

Purpose of the Study:

• To develop a high-throughput pipeline for alignment quality assessment and data filtering.
• To enable adaptable stringency criteria for alignment quality and missing data.
• To facilitate exploration of phylogenetic inference consistency with varying missing data levels.

Main Methods:

• Developed a flexible, high-throughput pipeline for genetic data processing.
• Implemented automated alignment quality assessment based on specified criteria.
• Filtered exonic sequence data for subsequent phylogenetic inference.

Main Results:

• Significantly reduced the need for manual visual inspection of alignments.
• Provided a rapid method for alignment filtering and quality control.
• Enabled exploration of phylogenetic estimation consistency across methods and missing data levels.

Conclusions:

• The pipeline offers an efficient approach to handling large-scale phylogenomic data.
• Facilitates robust evolutionary relationship inference by addressing alignment quality and missing data.
• Supports further investigation into the impact of data filtering on phylogenetic results.