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codon-usage

Here are 43 public repositories matching this topic...

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Edinburgh-Genome-Foundry / python_codon_tables

📊 Codon usage tables in code-friendly format + Python bindings

bioinformatics synbio codon-optimization codon-usage

Updated May 9, 2025
Python

Koeng101 / dnadesign

A lua package for designing DNA.

go bioinformatics synthetic-biology computational-biology sam genbank fasta fastq molecular-biology synbio rna-folding goldengate dna-barcode plasmids codon-optimization codon-usage pileup genetic-engineering dna-folding

Updated Jul 8, 2026
Go

SouradiptoC / CodonU

A python project for analysis of codon usage for gene or genome analysis

bioinformatics genome enc genome-analysis bioinformatics-analysis cai tai cbi bioinformatics-tool codon-usage codon codon-bias rscu codonw

Updated Nov 10, 2024
Python

alondmnt / codon-bias

Python package of codon usage bias analysis tools

python bioinformatics computational-biology codons codon-usage codon-bias codon-models

Updated May 16, 2026
Python

IQTLabs / freqgen

🎯 Generate DNA sequences with specified amino acid, codon, and k-mer frequencies

genetic-algorithm fasta kmer codon-usage

Updated Jan 23, 2023
Python

Kalan-Lab / codoff

codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, prophage, etc.) relative to the full genome.

horizontal-gene-transfer phage gene-clusters codon-usage biosynthetic-gene-clusters mobile-genetic-elements

Updated Jan 19, 2026
Python

rhondene / Codon-Usage-in-Python

Python3 command-line and GUI tools for common codon usage statistics given a FASTA of Coding sequences

bioinformatics codon-usage codon-bias synonymous-codons rscu optimal-codons

Updated Dec 9, 2025
Python

tdseher / simple-codon-optimizer

Simple Python program to perform codon optimization or heterology calculations.

protein-sequences dna-sequences codons codon-optimization codon-usage codon-bias codon-frequencies codon-optimizer

Updated Apr 13, 2021
Python

mt1022 / cubar

R Package for Codon Usage Bias Analysis. Comprehensive documentation and tutorials are available at:

machine-learning bioinformatics r-package sequence-analysis codon-usage

Updated Oct 29, 2025
R

smsaladi / codonw-slim

A slimmed down fork of CodonW with python bindings

bioinformatics dna protein codon-usage python-binding

Updated May 4, 2023
C

Mordziarz / RSCUcaller

Program in R for calculating RSCU.

bioinformatics genetics dna sequence codons codon-usage rscu rscucaller

Updated Jan 21, 2026
R

Maximato / Codonopt

Codonopt program is designed for codon optimization of protein sequences. The core of it based on the mathematical codon optimization proposed by Şen et al. (2020)

codon-optimization codon-usage codon-pairs-usage

Updated Apr 8, 2021
Python

enovoa / codonUsageToolkit

Toolkit to analyze codon usage bias

codon-usage codon-bias

Updated Dec 16, 2022
R

lindechun / CodonM

Comparative analysis pipeline of Population's Codon Usage

codon-usage codon-pattern codon-bias population-codonusage

Updated Jun 14, 2023
Python

Bohdan-Khomtchouk / Gaussian-distributed-codon-frequencies-of-genomes

Source code to accompany manuscript entitled "Gaussian-distributed codon frequencies of genomes" (Khomtchouk & Nonner, 2019)

genomics evolution genetic-code codon-usage

Updated Feb 3, 2019
D

smsaladi / codonpair

A codon pair score/codon pair bias calculator

bioinformatics codon-usage

Updated Feb 28, 2020
Perl

gxelab / cubat

Currently, we don't have the bandwidth to update and maintain the Python version; please use the R version instead. (https://github.com/mt1022/cubar)

python machine-learning bioinformatics genomics analysis codon-usage

Updated Oct 4, 2023
Python

alondmnt / codon-usage

MATLAB package for codon usage bias and NGS analysis

python bioinformatics computational-biology codons codon-usage codon-bias codon-models

Updated Feb 18, 2023
MATLAB

ostash-group / GeneticPlotter

A tool with nice GUI to visualize the codon usage frequencies in whole genomes

python gui tta codon-usage streptomyces

Updated Feb 2, 2021
Python

cmc-aau / gTranslate

Tool for identifying the genetic translation table used by prokaryotic organisms

machine-learning bioinformatics bacteria amino-acids codon-usage

Updated May 27, 2026
Python

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