No so HoT - heads or tails is not able to reliably compare multiple sequence alignments

Area of Science:

• Bioinformatics
• Computational Biology
• Evolutionary Biology

Background:

• Phylogenetic tree construction relies heavily on multiple sequence alignments (MSAs).
• The Heads or Tails methodology was proposed to evaluate MSA quality by comparing forward and reverse sequence alignments.
• Assessing MSA accuracy is crucial for reliable phylogenetic inference.

Purpose of the Study:

• To investigate the efficacy of the Heads or Tails methodology for assessing multiple sequence alignment quality.
• To determine if comparing forward and reverse alignments adequately captures the variability in MSAs.
• To evaluate the suitability of Heads or Tails for improving phylogenetic tree building.

Main Methods:

• Analysis of pairwise alignments as a special case of MSAs.
• Utilized a modified global alignment application to examine forward and reverse alignments.
• Investigated the space of possible alignments and potential variations.

Main Results:

• Forward and reverse alignments, even when identical, do not encompass all possible alignment variations.
• Differences between forward and reverse alignments indicate the presence of unaccounted-for alternative alignments.
• The Heads or Tails method is inadequate for capturing the full spectrum of MSA variability.
• MSA applications struggle to sample the complete space of possible alignments.
• Highly similar sequences are preferable for phylogenetic analysis due to fewer alternative alignments.

Conclusions:

• The Heads or Tails methodology is not suitable for assessing multiple sequence alignment accuracy.
• Limitations in MSA algorithms prevent adequate sampling of alignment possibilities.
• The Hall methodology may generate synthetic MSAs that are difficult for current aligners to recover.
• Sequence sets with higher similarity are recommended for robust phylogenetic tree construction.