Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

Area of Science:

• Bioinformatics
• Computational Biology
• Evolutionary Biology

Background:

• Multiple sequence alignments are crucial for phylogenetic analysis.
• Poorly conserved or divergent regions can introduce noise and inaccuracies.
• Manual editing of alignments is time-consuming and difficult to automate.

Purpose of the Study:

• To develop a computerized method for eliminating poorly aligned and divergent regions from multiple sequence alignments.
• To minimize the loss of informative sites during alignment refinement.
• To improve the suitability of alignments for phylogenetic analysis.

Main Methods:

• A novel computerized method was developed to select conserved blocks of positions.
• Selection criteria included contiguous conserved positions, minimal gaps, and conserved flanking regions.
• The method was tested on alignments of 10 mitochondrial proteins from diverse eukaryotic genomes.

Main Results:

• The computerized method effectively removed divergent segments, with higher removal rates in more divergent alignments.
• Post-removal, sequences showed more uniform amino acid composition and reduced pairwise distances.
• Phylogenetic trees derived from refined alignments showed altered topologies, particularly for poorly resolved nodes, supporting animal-fungi clades.

Conclusions:

• The computerized method automates alignment refinement, reducing manual editing needs.
• This facilitates large-scale phylogenetic analyses and improves reproducibility.
• The method enhances the reliability of phylogenetic inferences, especially for complex datasets.