Skip to content

codon.pl

Author: Abhinav Mishra

Name

codon.pl — compute codon usage and nucleotide composition metrics for one FASTA record.

Synopsis

perl scripts/codon.pl <in.fasta> <out.txt>

Description

Calculates nucleotide counts, GC/AT percentages and skews, dinucleotide/codon counts, RSCU, ENc, amino-acid composition, ORF statistics, sliding-window GC, and 3-mer entropy.

Options

  • in.fasta: input FASTA with one sequence record.
  • out.txt: metrics output text file.

Input/Output

  • Input: single-record DNA FASTA.
  • Output: plain-text metrics report (*.metrics.txt).

Author

Abhinav Mishra (mishraabhinav36@gmail.com)

Copyright (c) 2025 Abhinav Mishra. BSD 3-Clause.