Description:

freqgen 0.1.0

# Freqgen
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<img src=’https://raw.githubusercontent.com/Lab41/freqgen/master/logo/Freqgen2-01_icon_only.png’ height=”150”>
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[](https://travis-ci.org/Lab41/freqgen) [](https://freqgen.readthedocs.io/en/latest/?badge=latest) [](https://www.codefactor.io/repository/github/lab41/freqgen)
Freqgen is a tool to generate coding DNA sequences with specified amino acid
usage frequencies or sequence, GC content, codon usage bias, and/or k-mer
usage bias. To accomplish this, Freqgen uses genetic algorithms to efficiently
search the solution space of possible DNA sequences to find ones that most
closely match the desired parameters.
## Features

CLI and Python API
Can simultaneously match multiple DNA statistics
Built-in visualization utility
Supports several fitness metrics (and you can bring your own!)

## Installation
Simply run:

$ pip install freqgen

Or, to get the latest (but not necessarily stable) development version:

$ pip install git+https://github.com/Lab41/freqgen.git

## Five-second CLI tutorial
The basic flow of Freqgen can be summarized in three steps:
1. Generate a new amino acid sequence based on the amino acid usage profile of
reference sequences. If you already have a specific amino acid sequence in mind
(i.e. for synthetic biology uses), skip this step:

$ freqgen aa reference_sequences.fna -o new_sequence.faa -l LENGTH

2. Create a YAML file containing k-mer frequencies for the amino acid
sequence’s DNA to have:

$ freqgen featurize reference_sequences.fna -k INT -o reference_freqs.yaml


Generate the DNA sequence coding for the amino acid sequence:

$ freqgen -t reference_freqs.yaml -s new_sequence.faa -v -o optimized.fna


Visualize the results of the optimization (optional):

$ freqgen visualize –target reference_freqs.yaml –optimized optimized.fna



## Documentation
Read the full docs over at
[freqgen.readthedocs.io](http://freqgen.readthedocs.io).
## Citation
To be determined!

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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