PAL2NAL

PAL2NAL constructs multiple codon alignments from aligned protein sequences and their corresponding DNA (or mRNA) sequences to enable analysis of nucleotide substitution types and rates in coding DNA and assessment of selective constraints and DNA-based phylogenetic relationships.

Key Features:

• Codon alignment construction: Generates codon alignments from aligned protein sequences paired with corresponding DNA (or mRNA) sequences, handling mismatches between protein and DNA sequences as well as untranslated regions and polyA tails.
• Handling of genetic anomalies: Accommodates frame shifts and in-frame stop codons, allowing analysis of sequences such as pseudogenes.
• Customizable analysis regions: Allows specification of subregions of the input alignment for targeted analysis of functional domains or specific exons.

Scientific Applications:

• Selective constraint analysis: Supports examination of synonymous (Ks) and non-synonymous (Ka) substitution rates to infer selective pressures on genes.
• Phylogenetic studies: Produces codon alignments suitable for DNA-based phylogenetic analyses to investigate evolutionary relationships among species.

Methodology:

PAL2NAL takes aligned protein sequences and their corresponding DNA (or mRNA) sequences as inputs and processes them to generate a multiple codon alignment while accommodating mismatches, untranslated regions, polyA tails, frame shifts, and in-frame stop codons.