cdskit degeneracy

cdskit degeneracy extracts aligned nucleotide positions by codon degeneracy class.

Example

cdskit degeneracy --seq_file alignment.fasta --prefix genes --fold 4 2 --codon_table 1

This writes separate files such as genes_4fold_positions.fasta and genes_2fold_positions.fasta.

What it does

• Examines each aligned codon column.
• Classifies each nucleotide position as 0, 2, 3, or 4 fold degenerate when the assignment is consistent across usable sequences.
• Skips positions that are unassigned or conflicting across sequences.

Key options

• --prefix PATH: Output filename prefix.
• --fold 0 2 3 4: Degeneracy class or classes to export.
• --codon_table INT: NCBI codon table ID used for degeneracy classification.
• --report PATH: Optional JSON or TSV summary report.

Notes

• Input sequences must be DNA, aligned, and multiples of three in length.
• Output alignments preserve sequence order while retaining only the selected nucleotide positions.

Citation

No separate method paper is designated for this utility. Report the CDSKIT version, command and options; see citing CDSKIT.