Metadata-Version: 2.1
Name: CodonU
Version: 1.1.2
Summary: An integrated package for codon usage analysis
Home-page: https://github.com/SouradiptoC/codon_usage
Author: Souradipto Choudhuri
Author-email: Souradipto <sourochaudhuri@gmail.com>
License: MIT License
        
        Copyright (c) 2023 Souradipto Choudhuri
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Project-URL: Bug Tracker, https://github.com/SouradiptoC/codon_usage/issues
Project-URL: Documentation, https://codonu.readthedocs.io/en/latest/?badge=latest
Project-URL: Source Code, https://github.com/SouradiptoC/codon_usage
Keywords: bioinformatics,bioinformatics-analysis,bioinformatics-tool,codon-usage,codon,codon-bias,genomic-analysis,genome,codonW,tAI
Classifier: Development Status :: 5 - Production/Stable
Classifier: Natural Language :: English
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Science/Research
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE.md
Requires-Dist: biopython ~=1.79
Requires-Dist: numpy ~=1.24.2
Requires-Dist: pandas ~=2.1.1
Requires-Dist: matplotlib >=3.6.3
Requires-Dist: scipy ~=1.10.0
Requires-Dist: prince ~=0.12.1
Requires-Dist: gtAI ~=1.0.4

[//]: # (# CodonU)

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# Introduction

Welcome to CodonU!

This is an integrated package for codon usage analysis.

# Functionalities

Various functionalities can be found below. For gene/genome analysis, this package can:

- For Nucleotide sequences
    - Calculate RSCU
    - Calculate CAI
    - Calculate CBI
    - Calculate ENc
    - Calculate tAI
- For Protein sequences
    - Calculate Aromaticity
    - Calculate gravy

One can also can calculate the multivariate analysis, popularly known as correspondence analysis (COA) for the codons
easily.
Supported calculations are:

- For Nucleotide sequences
    - COA using codon frequency with scale set to length of gene
    - COA using codon RSCU values with scale set to length of gene
- For Protein sequences
    - COA using amino acid frequency with scale set to gravy score
    - COA using amino acid frequency with scale set to aromaticity score

Phylogenetic analysis and tree building now can be done.

Detailed instructions on how to use the functions can be found in
the [examples](https://github.com/SouradiptoC/CodonU/tree/master/Examples)

# Installation

    pip install CodonU

# Future Plans

None. If you would like recommend one, please mail
at [sourochaudhuri@gmail.com](mailto:sourochaudhuri@gmail.com)

