Clustal 1.8 (Clustal W, Clustal X)

Clustal 1.8 (Clustal W, Clustal X) performs multiple sequence alignment of protein and nucleotide sequences to produce accurate alignments for comparative and evolutionary analyses, including phylogenetic tree calculation.

Key Features:

• Sequence weighting: Assigns individual weights to each sequence within partial alignments to down-weight near-duplicate sequences and up-weight more divergent sequences.
• Variable substitution matrices: Varies amino acid substitution matrices at different stages of alignment based on sequence divergence.
• Residue-specific gap penalties: Employs residue-specific gap penalties and reduces gap penalties locally in hydrophilic regions to favor gaps in potential loop regions.
• Locally reduced gap penalties: Applies locally reduced gap penalties at positions where gaps have been opened in early alignments to promote additional gap opening at those positions.
• Multiple sequence and profile alignment: Supports both multiple sequence alignment and profile alignment capabilities.
• Alignment quality analysis: Provides analysis to identify low-scoring segments and exceptional residues for refinement and error detection in input sequences.
• Phylogenetic tree calculation: Allows calculation of phylogenetic trees from alignments to support evolutionary analysis.
• Output formats: Supports export of alignments in formats including NEXUS and FASTA.

Scientific Applications:

• Evolutionary studies: Produces alignments and trees used to infer evolutionary relationships among sequences.
• Comparative genomics: Aligns protein and nucleotide sequences for comparative analyses across species or gene families.
• Functional genomics: Supports identification of conserved residues and regions relevant to function through refined alignments.
• Alignment quality assessment and error detection: Identifies low-scoring segments and exceptional residues to detect potential input-sequence errors and refine difficult alignments.

Methodology:

Assigns sequence weights in partial alignments; varies amino acid substitution matrices according to sequence divergence; applies residue-specific and locally reduced gap penalties, including reduced penalties in hydrophilic regions and at positions with gaps opened in early alignments; supports multiple sequence and profile alignment; calculates phylogenetic trees and exports alignments in NEXUS and FASTA formats.