PnpProbs: a better multiple sequence alignment tool by better handling of guide trees

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Developing accurate multiple sequence alignment (MSA) tools is crucial for evolutionary and functional analyses.
• Existing MSA methods often struggle with sequences of varying evolutionary distances.
• Guide trees are essential for progressive alignment but can be suboptimal for distantly related sequences.

Purpose of the Study:

• Introduce PnpProbs, a new MSA tool designed to enhance alignment quality.
• Address limitations of current MSA tools in handling sequences with diverse relatedness.
• Improve the accuracy of phylogenetic analyses derived from sequence alignments.

Main Methods:

• PnpProbs classifies sequences into normally and distantly related groups.
• For normally related sequences, an adaptive guide tree construction method is employed based on sequence discrepancy.
• For distantly related sequences, PnpProbs utilizes non-progressive alignment techniques, bypassing guide trees.

Main Results:

• PnpProbs demonstrated superior alignment scores compared to thirteen other popular MSA tools across most tests.
• Phylogenetic trees generated using PnpProbs alignments showed higher concordance with model trees.
• The tool's adaptive strategy effectively improves alignment quality for diverse sequence sets.

Conclusions:

• PnpProbs integrates progressive and non-progressive alignment strengths for robust MSA.
• The developed tool consistently produces high-quality alignments, outperforming existing methods.
• PnpProbs offers a significant advancement for sequence alignment and subsequent phylogenetic studies.