MaxAlign

MaxAlign maximizes the number of nucleotide or amino acid symbols in gap-free columns of alignments to optimize sequence alignments for phylogenetic and other bioinformatical analyses.

Key Features:

• Gap-free symbol maximization: Maximizes the count of nucleotide or amino acid symbols present in gap-free columns within an alignment.
• Sequence exclusion optimization: Selects an optimal subset of sequences to exclude in order to reduce gapped columns and increase usable data.
• Support for nucleotide and amino acid alignments: Operates on both nucleotide and amino acid sequence alignments.
• Detection of problematic sequences: Identifies misaligned or defective sequences for exclusion without manual inspection.
• Improves phylogenetic estimates: Enhances accuracy of phylogenetic reconstruction when gapped columns are excluded after processing.
• Normalized Symmetric Similarity (NSS): Implements the NSS measure for comparing and validating tree topologies.
• Empirical performance: Demonstrated effectiveness in improving alignment quality and downstream phylogenetic accuracy in comparative evaluations.

Scientific Applications:

• Phylogenetic reconstruction: Improves input alignments for more accurate phylogenetic tree estimation.
• Alignment quality improvement: Increases the amount of gap-free data available for downstream analyses.
• Quality control of sequence datasets: Detects and removes misaligned or defective sequences that reduce analysis reliability.
• Tree topology comparison and validation: Uses NSS to compare and validate alternative phylogenetic trees.

Methodology:

Optimizes alignments by selecting an optimal subset of sequences to exclude to maximize nucleotide or amino acid symbols in gap-free columns and computes Normalized Symmetric Similarity (NSS) for comparing tree topologies.