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License](https://img.shields.io/pypi/l/CodonU)](https://opensource.org/licenses/MIT)\n[![DOI](https://zenodo.org/badge/536583655.svg)](https://zenodo.org/badge/latestdoi/536583655)\n[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/CodonU)](https://pypi.org/project/CodonU)\n[![PyPI](https://img.shields.io/pypi/v/CodonU)](https://pypi.org/project/CodonU)\n[![PyPI - Format](https://img.shields.io/pypi/format/CodonU)](https://pypi.org/project/CodonU)\n[![Downloads](https://static.pepy.tech/personalized-badge/codonu?period=total\u0026units=international_system\u0026left_color=grey\u0026right_color=blue\u0026left_text=Downloads)](https://pepy.tech/project/codonu)\n[![CodeFactor](https://www.codefactor.io/repository/github/souradiptoc/codonu/badge/master)](https://www.codefactor.io/repository/github/souradiptoc/codonu/overview/master)\n[![Documentation Status](https://readthedocs.org/projects/codonu/badge/?version=latest)](https://codonu.readthedocs.io/en/latest/?badge=latest)\n\n# Introduction\n\nWelcome to CodonU!\n\nThis is an integrated package for codon usage analysis. To know more about motivation and workflow, please read\nthe [Thesis](https://doi.org/10.5281/zenodo.8154433) or the [Paper](https://doi.org/10.1109/TCBB.2023.3335823). The documentation is\navailable [here](https://codonu.readthedocs.io/en/latest/?badge=latest).\n\n# What's New (As of September 23rd, 2023)\n\nNow you can analyze tRNA adaptation index\n\n# Functionalities\n\nVarious functionalities can be found below. For gene/genome analysis, this package can:\n\n- For Nucleotide sequences\n    - Calculate RSCU\n    - Calculate CAI\n    - Calculate CBI\n    - Calculate ENc\n    - Calculate tAI\n- For Protein sequences\n    - Calculate Aromaticity\n    - Calculate gravy\n\nOne can also calculate the multivariate analysis, popularly known as correspondence analysis (COA) for the codons\neasily.\nSupported calculations are:\n\n- For Nucleotide sequences\n    - COA using codon frequency for codons and genes\n    - COA using codon RSCU values for codons and genes\n- For Protein sequences\n    - COA using amino acid frequency with scale set to gravy score\n    - COA using amino acid frequency with scale set to aromaticity score\n\nPhylogenetic analysis and tree building now can be done.\n\nDetailed instructions on how to use the functions can be found in\nthe [examples](https://github.com/SouradiptoC/CodonU/tree/master/Examples)\n\n# Graphics!!\n\nAlso, can generate beautiful graphics for publication purposes or otherwise. Some plots are:\n\nENc plot for human chromosome 2\n\n![ENc plot for human chromosome 2](https://github.com/SouradiptoC/CodonU/blob/master/images/ENc_plot_Human%20Cr%202.png)\n\nNeutrality plot for human chromosome 2\n\n![Neutrality plot for human chromosome 2](https://github.com/SouradiptoC/CodonU/blob/master/images/Neutrality_plot_Human%20Cr%202.png)\n\nCOA of Codon frequency for codons\n![COA of Codon frequency for codons](https://github.com/SouradiptoC/CodonU/blob/master/images/CA_codon_freq_codon_Staphylococcus_aureus.png)\n\nCOA of Codon frequency for genes\n![COA of Codon frequency for genes](https://github.com/SouradiptoC/CodonU/blob/master/images/CA_codon_freq_gene_Staphylococcus_aureus.png)\n\nComparative analysis of codon COA\n![Comparative analysis of codon COA](https://github.com/SouradiptoC/CodonU/blob/master/images/gene_coa_compare.png)\n\nCOA of aa frequency for genes with scale set to GRAVY\n![COA of aa frequency for genes with scale set to GRAVY](https://github.com/SouradiptoC/CodonU/blob/master/images/CA_aa_freq_aa_Staphylococcus_aureus.png)\n\nExamples of other plots can be found in the [images](https://github.com/SouradiptoC/CodonU/tree/master/images)\n\n# Installation\n\n    pip install CodonU\n\n# Future Plans\n\nNone. If you would like to recommend one, please mail\nat [sourochaudhuri@gmail.com](mailto:sourochaudhuri@gmail.com)\n\n# Citation\n\nPlease cite the article as\n\n    @ARTICLE{10330762,\n        author={Choudhuri, Souradipto and Sau, Keya},\n        journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, \n        title={CodonU: A Python Package for Codon Usage Analysis}, \n        year={2024},\n        volume={21},\n        number={1},\n        pages={36-44},\n        keywords={Amino acids;Indexes;Bioinformatics;Software;Web servers;Proteins;Phylogeny;Codon bias;codon usage;codon usage analysis;CodonW;correspondence analysis;phylogenetic analysis;tRNA analysis},\n        doi={10.1109/TCBB.2023.3335823}\n    }\n\n\nPlease cite the software as\n\n    @software{choudhuri_souradipto_2023_7868197,\n        author={Choudhuri, Souradipto},\n        title={CodonU},\n        month=apr,\n        year=2023,\n        publisher={Zenodo},\n        version={v1.0.4},\n        doi={10.5281/zenodo.7868197},\n        url={https://doi.org/10.5281/zenodo.7868197}\n    }\n\n# Reference\n\n* J. L. Bennetzen and B. D. Hall, “Codon selection in yeast.,” Journal of Biological Chemistry, vol. 257, no. 6, pp.\n  3026–3031, Mar. 1982,\n  doi: [10.1016/s0021-9258(19)81068-210.1016/s0021-9258(19)81068-2](https://doi.org/10.1016/S0021-9258(19)81068-2).\n* F. Wright, “The ‘effective number of codons’ used in a gene,” Gene, vol. 87, no. 1, pp. 23–29, Mar. 1990,\n  doi: [10.1016/0378-1119(90)90491-9](https://doi.org/10.1016/0378-1119(90)90491-9).\n* A. Fuglsang, “The ‘effective number of codons’ revisited,” Biochemical and Biophysical Research Communications, vol.\n  317, no. 3, pp. 957–964, May 2004, doi: [10.1016/j.bbrc.2004.03.138](https://doi.org/10.1016/j.bbrc.2004.03.138).\n* P. M. Sharp and W.-H. Li, “The codon adaptation index-a measure of directional synonymous codon usage bias, and its\n  potential applications,” Nucleic Acids Research, vol. 15, no. 3, pp. 1281–1295, 1987,\n  doi: [10.1093/nar/15.3.1281](https://doi.org/10.1093/nar/15.3.1281).\n* J. Kyte and R. F. Doolittle, “A simple method for displaying the hydropathic character of a protein,” Journal of\n  Molecular Biology, vol. 157, no. 1, pp. 105–132, May 1982,\n  doi: [10.1016/0022-2836(82)90515-0](https://doi.org/10.1016/0022-2836(82)90515-0).\n* J. R. Lobry and C. Gautier, “Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in\n  999 Escherichia coli chromosome-encoded genes,” Nucleic Acids Research, vol. 22, no. 15, pp. 3174–3180, Aug. 1994,\n  doi: [10.1093/nar/22.15.3174](https://doi.org/10.1093/nar/22.15.3174).\n* J. R. Lobry, Multivariate Analyses of Codon Usage Biases. ISTE Press - Elsevier, 2018.\n  doi: [10.1016/C2018-0-02165-9](https://doi.org/10.1016/C2018-0-02165-9).\n* F. Sievers and D. G. Higgins, “Clustal Omega for making accurate alignments of many protein sequences,” Protein\n  Science, vol. 27, no. 1, pp. 135–145, Jan. 2018, doi: [10.1002/pro.3290](https://doi.org/10.1002/pro.3290).\n* M. A. Larkin et al., “Clustal W and Clustal X version 2.0,” Bioinformatics, vol. 23, no. 21, pp. 2947–2948, Nov. 2007,\n  doi: [10.1093/bioinformatics/btm404](https://doi.org/10.1093/bioinformatics/btm404).\n* Anwar et al., \"gtAI: an improved species-specific tRNA adaptation index using the genetic algorithm\", Frontiers in\n  Molecular Biosciences, vol. 10, Jul. 2023,\n  doi: [10.3389/fmolb.2023.1218518](https://doi.org/10.3389/fmolb.2023.1218518)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsouradiptoc%2Fcodonu","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsouradiptoc%2Fcodonu","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsouradiptoc%2Fcodonu/lists"}