Table of Contents
2021 https://github.com/haruosuz/codon
http://rpubs.com/dbg Daniel Bryan Goodman
http://rpubs.com/dbg/3350 Step 07 - Looking at Codon and tRNA Adaptation Indices
http://rpubs.com/dbg/3351 Step 10 - Looking at amino acid and codon usage
https://cran.r-project.org/package=seqinr
https://seqinr.r-forge.r-project.org/
https://search.r-project.org/CRAN/refmans/seqinr/html/00Index.html cai Codon Adaptation Index https://search.r-project.org/CRAN/refmans/seqinr/html/cai.html
cai(seq, w, numcode = 1, zero.threshold = 0.0001, zero.to = 0.01)
tRNA adaptation index (tAI)
https://github.com/haruosuz/codon/blob/master/README.md#tai
https://cran.r-project.org/package=tAI tAI: The tRNA Adaptation Index
Published: 2025-04-16
Commits on Apr 25, 2025 https://github.com/mariodosreis/tai REFERENCES
https://www.bioconductor.org/packages/tRNA/
Ernst F (2022). tRNA: Analyzing tRNA sequences and structures. R package version 1.14.0.
HTML R Script tRNA https://www.bioconductor.org/packages/release/bioc/vignettes/tRNA/inst/doc/tRNA.html Analyzing tRNA sequences and structures Felix G.M. Ernst 2022-04-26
https://www.bioconductor.org/packages/sscu/
The package calculates the indexes for selective stength in codon usage in bacteria species. (1) The package can calculate the strength of selected codon usage bias (sscu, also named as s_index) based on Paul Sharp's method.
Sun Y (2025). sscu: Strength of Selected Codon Usage. doi:10.18129/B9.bioc.sscu, R package version 2.40.0,
22 Aug 2018 https://arxiv.org/abs/1808.07259 [1808.07259] SSCU: an R/Bioconductor package for analyzing selective profile in synonymous codon usage https://arxiv.org/pdf/1808.07259 Additional files Supplementary File 1. The user manual for SSCU package.
Nov. 8, 2020 https://rdrr.io/bioc/sscu/f/vignettes/sscu.Rmd sscu user manual (2.4.0)
Literature https://github.com/haruosuz/codon/blob/master/README.md#sscu
https://github.com/xl0418/Phydon Phydon has several essential dependencies, including gRodon2, ape, Biostrings, picante, etc.
2025-05-07 https://pubmed.ncbi.nlm.nih.gov/40335538/ Nat Commun . 2025 May 7;16(1):4256. doi: 10.1038/s41467-025-59558-9. Improved maximum growth rate prediction from microbial genomes by integrating phylogenetic information Liang Xu 1, Emily Zakem 2, J L Weissman 3 4 https://www.nature.com/articles/s41467-025-59558-9 https://pmc.ncbi.nlm.nih.gov/articles/PMC12059116/
https://github.com/jlw-ecoevo/gRodon2
https://www.microbialgamut.com/gRodon-vignette Predicting maximal growth rates with gRodon
2022-10-26 https://pubmed.ncbi.nlm.nih.gov/36190138/ mSystems . 2022 Oct 26;7(5):e0074522. doi: 10.1128/msystems.00745-22. Epub 2022 Oct 3. Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics J L Weissman 1, Marie Peras 2, Tyler P Barnum 2, Jed A Fuhrman 1 https://journals.asm.org/doi/10.1128/msystems.00745-22 https://pmc.ncbi.nlm.nih.gov/articles/PMC9600850/ Code for all analyses presented can be found at: https://github.com/jlw-ecoevo/gRodon2-benchmarking. The R package gRodon with MMv2 implemented can be found at https://github.com/jlw-ecoevo/gRodon2.
2021-03-23 https://pubmed.ncbi.nlm.nih.gov/33723043/ Proc Natl Acad Sci U S A . 2021 Mar 23;118(12):e2016810118. doi: 10.1073/pnas.2016810118. Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns Jake L Weissman 1, Shengwei Hou 2, Jed A Fuhrman 2 https://www.pnas.org/content/118/12/e2016810118.long https://pmc.ncbi.nlm.nih.gov/articles/PMC8000110/ MATERIALS AND METHODS All scripts used to generate figures and analysis, as well as predicted growth rates for various genomic datasets and the full EGGO database, are available at https://github.com/jlw-ecoevo/eggo. The gRodon package, including documentation and a vignette, can be downloaded at https://github.com/jlw-ecoevo/gRodon.
http://bioconductor.org/packages/coRdon/ Tool for analysis of codon usage in various unannotated or KEGG/COG annotated DNA sequences. Calculates different measures of CU bias and CU-based predictors of gene expressivity, and performs gene set enrichment analysis for annotated sequences. Implements several methods for visualization of CU and enrichment analysis results.
Elek A, Kuzman M, Vlahovicek K (2025). coRdon: Codon Usage Analysis and Prediction of Gene Expressivity. doi:10.18129/B9.bioc.coRdon, R package version 1.28.0, https://bioconductor.org/packages/coRdon.
HTML R Script coRdon https://bioconductor.org/packages/release/bioc/vignettes/coRdon/inst/doc/coRdon.html Codon usage (CU) analysis in R Anamaria Elek 2025-10-29
2018-09-28 https://zir.nsk.hr/en/islandora/object/pmf%3A4815 https://repozitorij.unizg.hr/en/islandora/object/pmf%3A4815 MASTER'S THESIS coRdon: an R package for codon usage analysis and prediction of gene expressivity Anamaria Elek (2018)
2016 https://pubmed.ncbi.nlm.nih.gov/27115650/ Methods Mol Biol . 2016;1415:509-31. doi: 10.1007/978-1-4939-3572-7_26. Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles Maja Fabijanić 1, Kristian Vlahoviček 2 https://link.springer.com/protocol/10.1007%2F978-1-4939-3572-7_26
2013-10 https://pubmed.ncbi.nlm.nih.gov/23921637/ Nucleic Acids Res . 2013 Oct;41(19):8842-52. doi: 10.1093/nar/gkt673. Epub 2013 Aug 5. Environmental shaping of codon usage and functional adaptation across microbial communities Masa Roller 1, Vedran Lucić, István Nagy, Tina Perica, Kristian Vlahovicek https://academic.oup.com/nar/article/41/19/8842/1198641 https://pmc.ncbi.nlm.nih.gov/articles/PMC3799439/
https://phylogenomics.blogspot.jp/2013/08/great-use-of-metagenomic-data-community.html August 09, 2013 Great use of metagenomic data: community wide adaptation signatures
https://cran.r-project.org/package=vhica vhica: Vertical and Horizontal Inheritance Consistence Analysis
The "Vertical and Horizontal Inheritance Consistence Analysis" method is described in the following publication: "VHICA: a new method to discriminate between vertical and horizontal transposon transfer: application to the mariner family within Drosophila" by G. Wallau. et al. (2016) doi:10.1093/molbev/msv341. The purpose of the method is to detect horizontal transfers of transposable elements, by contrasting the divergence of transposable element sequences with that of regular genes.
Version: 0.2.7
Published: 2020-03-02
Maintainer: Arnaud Le Rouzic
https://cran.r-project.org/web/packages/vhica/vhica.pdf April 5, 2016
https://rdrr.io/cran/vhica/man/CUB.html https://www.rdocumentation.org/packages/vhica/versions/0.2.4/topics/CUB
CUB: Computes the Codon Usage Bias of DNA sequences
The function reads aligned sequences in a fasta file and estimates the codon usage bias for each sequence. Several methods exist to estimate CUB; so far, only the "Effective Number of Codons" (ENC) calculation is available.
file FASTA file in which aligned sequences are stored.
sequence Alternatively, the result of seqinr::read.fasta.
Warning message:
In .checkseq(sequence, gene.name = if (is.null(file)) "" else file) :
Sequences do not have the same length. Adding as many n as necessary.
https://cran.r-project.org/package=vhcub vhcub: Virus-Host Codon Usage Co-Adaptation Analysis Analyze the co-adaptation of codon usage between a virus and its host, calculate various codon usage bias measurements as: effective number of codons (ENc) Novembre (2002) doi:10.1093/oxfordjournals.molbev.a004201, codon adaptation index (CAI) Sharp and Li (1987) doi:10.1093/nar/15.3.1281, relative codon deoptimization index (RCDI) Puigbò et al (2010) doi:10.1186/1756-0500-3-87, similarity index (SiD) Zhou et al (2013) doi:10.1371/journal.pone.0077239, synonymous codon usage orderliness (SCUO) Wan et al (2004) doi:10.1186/1471-2148-4-19 and, relative synonymous codon usage (RSCU) Sharp et al (1986) doi:10.1093/nar/14.13.5125. Also, it provides a statistical dinucleotide over- and underrepresentation with three different models. Implement several methods for visualization of codon usage as ENc.GC3plot() and PR2.plot().
Version: 1.0.0 Imports: Biostrings, coRdon , ggplot2, seqinr, stringr Suggests: testthat Published: 2019-11-15 Author: Ali Mostafa Anwar [aut, cre], Mohamed Soudy [aut] Maintainer: Ali Mostafa Anwar <ali.mo.anwar at std.agr.cu.edu.eg>
https://search.r-project.org/CRAN/refmans/vhcub/html/00Index.html CAI.values Codon Adaptation Index (CAI) https://search.r-project.org/CRAN/refmans/vhcub/html/CAI.values.html
CAI.values(df.virus, ENc.set.host,
df.host,genetic.code = "1",set.len = 5, threshold = 0)
https://pubmed.ncbi.nlm.nih.gov/32274012/ F1000Res . 2019 Dec 23;8:2137. doi: 10.12688/f1000research.21763.1. eCollection 2019. vhcub: Virus-host codon usage co-adaptation analysis Ali Mostafa Anwar 1, Mohamed Soudy 2, Radwa Mohamed 1 https://f1000research.com/articles/8-2137/v1 https://pmc.ncbi.nlm.nih.gov/articles/PMC7104870/
Unpublished?
https://cran.r-project.org/package=SADEG SADEG: Stability Analysis in Differentially Expressed Genes We analyzed the nucleotide composition of genes with a special emphasis on stability of DNA sequences. Besides, in a variety of different organisms unequal use of synonymous codons, or codon usage bias, occurs which also show variation among genes in the same genome. Seemingly, codon usage bias is affected by both selective constraints and mutation bias which allows and enables us to examine and detect changes in these two evolutionary forces between genomes or along one genome. Therefore, we determined the codon adaptation index (CAI), effective number of codons (ENC) and codon usage analysis with calculation of the relative synonymous codon usage (RSCU), and subsequently predicted the translation efficiency and accuracy through GC-rich codon usages. Furthermore, we estimated the relative stability of the DNA sequence following calculation of the average free energy (Delta G) and Dimer base-stacking energy level.
Published: 2017-01-13
Reference manual: SADEG.pdf https://cran.r-project.org/web/packages/SADEG/SADEG.pdf
https://search.r-project.org/CRAN/refmans/SADEG/html/00Index.html SADEG.CAI SADEG.CAI https://search.r-project.org/CRAN/refmans/SADEG/html/SADEG.CAI.html
SADEG.CAI(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")
https://cran.r-project.org/package=cubfits cubfits: Codon Usage Bias Fits Estimating mutation and selection coefficients on synonymous codon bias usage based on models of ribosome overhead cost (ROC). Multinomial logistic regression and Markov Chain Monte Carlo are used to estimate and predict protein production rates with/without the presence of expressions and measurement errors. Work flows with examples for simulation, estimation and prediction processes are also provided with parallelization speedup. The whole framework is tested with yeast genome and gene expression data of Yassour, et al. (2009) doi:10.1073/pnas.0812841106.
Version: 0.1-4
Published: 2021-11-07
Reference manual: cubfits.pdf https://cran.r-project.org/web/packages/cubfits/cubfits.pdf
Vignettes: cubfits-guide https://cran.r-project.org/web/packages/cubfits/vignettes/cubfits-guide.pdf A Quick Guide for the cubfits Package (Ver. 0.1-2)
https://search.r-project.org/CRAN/refmans/cubfits/html/t4_cai.html
calc_cai_values(y, y.list, w = NULL)
https://pubmed.ncbi.nlm.nih.gov/19208812/ Proc Natl Acad Sci U S A . 2009 Mar 3;106(9):3264-9. doi: 10.1073/pnas.0812841106. Epub 2009 Feb 10. Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing Moran Yassour 1, Tommy Kaplan, Hunter B Fraser, Joshua Z Levin, Jenna Pfiffner, Xian Adiconis, Gary Schroth, Shujun Luo, Irina Khrebtukova, Andreas Gnirke, Chad Nusbaum, Dawn-Anne Thompson, Nir Friedman, Aviv Regev
https://pubmed.ncbi.nlm.nih.gov/15374859/ Bioinformatics . 2005 Feb 15;21(4):545-7. doi: 10.1093/bioinformatics/bti037. Epub 2004 Sep 16. Online synonymous codon usage analyses with the ade4 and seqinR packages D Charif 1, J Thioulouse, J R Lobry, G Perrière https://academic.oup.com/bioinformatics/article/21/4/545/203393
http://pbil.univ-lyon1.fr/datasets/charif04/ Synonymous codon usage analyse