GUIDANCE

GUIDANCE assesses confidence in multiple sequence alignments (MSAs) by quantifying column-, residue-, and sequence-level reliability to identify and remove unreliable regions for downstream comparative analyses.

Key Features:

• Input Flexibility: Accepts sets of unaligned sequences as input.
• Alignment Algorithm Choice: Supports alignment using ClustalW, MAFFT, and PRANK.
• Sequence Type Versatility: Handles nucleotide, protein, and codon sequences.
• Confidence Scoring and Visualization: Produces confidence scores and color-coded graphic visualizations for each column, residue, and sequence to identify and facilitate removal of unreliable regions.

Scientific Applications:

• Multiple sequence alignment refinement: Identifying and removing unreliable columns, residues, and sequences to improve alignment quality for downstream analyses.
• Phylogenetic analysis: Improving input alignments for phylogenetic reconstruction by reducing alignment uncertainty related to guide-tree variation.
• Functional and comparative sequence analyses: Reducing alignment-derived errors that can affect functional inference and comparative studies.

Methodology:

Implements the Heads-or-Tails (HoT) method to assess uncertainty from co‑optimal solutions and the GUIDANCE method to evaluate robustness of alignments to guide-tree uncertainty.