Metadata-Version: 2.1
Name: CodonU
Version: 1.0.3
Summary: This package is designed for helping in genomic analysis
Home-page: https://github.com/SouradiptoC/codon_usage
Author: Souradipto Choudhuri
Author-email: sourochaudhuri@gmail.com
License: MIT License
Project-URL: Bug Tracker, https://github.com/SouradiptoC/codon_usage/issues
Project-URL: Documentation, https://souradiptoc.github.io/CodonU/
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
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
Description-Content-Type: text/markdown
License-File: LICENSE.md

[//]: # (# CodonU)

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[![Docs](https://img.shields.io/badge/docs-passing-brightgreen)](https://souradiptoc.github.io/CodonU/)

# 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
- 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)
