P*R*O*P: a web application to perform phylogenetic analysis considering the effect of gaps

Area of Science:

• Bioinformatics
• Computational Biology
• Evolutionary Biology

Background:

• Phylogenetic analysis accuracy relies on evolutionary models.
• Existing models often neglect gap sites (insertions/deletions) in sequence alignments.
• Incorporating gap information can enhance phylogenetic estimates.

Purpose of the Study:

• Introduce a novel genetic difference measure that includes gap site information.
• Develop P*R*O*P, a web application for phylogenetic analysis using this new measure.
• Demonstrate the impact of gap information on phylogenetic tree topology.

Main Methods:

• Developed a new genetic distance metric considering gap sites.
• Created the P*R*O*P web application for phylogenetic analysis.
• Applied P*R*O*P to p53 amino acid sequences from 31 organisms.

Main Results:

• P*R*O*P was developed as a web application for phylogenetic analysis.
• Analysis showed that genetic differences with and without gap information yield different tree topologies.
• The study highlights the importance of gap sites in evolutionary modeling.

Conclusions:

• P*R*O*P is accessible online for phylogenetic analysis.
• The tool's key feature is estimating genetic differences without removing gap sites.
• This approach aids in detecting significant evolutionary differences.