BioGenie

BioGenie is a complete bioinformatics command line tool for macOS, GNU Linux and MS Windows, written in C++.

Important

BioGenie is now available on Conda. Visit the conda page.

It currently supports fasta formats(.fasta, .faa, .fa).

• To run the app, simply type:

biogenie <function> <filename>

• For example, to calculate GC percentage:

biogenie -gc example.fasta

Documentation

BioGenie uses functions to execute different tools for different applications. Read Documentation for more information (References included).

Pipelines:

• Nucleostats ---> "-nucleo". Statistics and metrics for DNA. Ideal for Primer design.
• Proteostats ---> "-prot". Statistics and protein structural properties.
• Assemblystats ---> "-asmbl". Statistics and metrics for genome assembly.
• Pairwise Global Sequence Alignment with Needleman-Wunsch ---> "-nw".
• Pairwise Local Sequence Alignment with Smith-Waterman ---> "-sw".

Tip

Assemblystats is in experimental phase. Always check your data first before evaluating your results.

Single commands:

• Get the complement DNA sequence ---> "-c".
• Get the reverse complement DNA sequence ---> "-rc".
• Get the codon number ---> "-nc".
• Get the mRNA ---> "-t".
• Motif search ---> "-mf".
• Ambiguous bases statistics ---> "-amb".
• GC percentage calculation ---> "-gc".
• Generate the aminoacids(Protein chain) ---> "-p".
• Generate the Protein chain with color ---> "-pc".
• Color the protein chain from a FASTA file ---> "-pca".
• Separate different sequencies in a FASTA file ---> "-ss".
• Print the different sequence headers from a FASTA file ---> "-sh".
• Trim DNA sequence ---> "-tr".
• Calculate the Number of Base Pairs(bp) ---> "-bp".
• Get the purine/pyrimidine ratio --> "-pp".
• Calculate melting temperature (Tm) of DNA sequences using the Wallace Rule(only valid for oligos <20bp) ---> "-mt1".
• Calculate melting temperature (Tm) of DNA sequences using the SantaLucia 1998 nearest-neighbor method ---> "-mt2".
• Calculate the Isoelectric Point of a protein ---> "-pi".
• Calculate the molecular weight of a protein(kDa) ---> "-mw".
• Calculate the Extinction Coefficient of a protein ---> "-ec".
• Coloured cDNA sequence ---> "-cc".
• Coloured DNA sequence ---> "-sc".
• Get the Open Reading Frame(ORF) ---> "-orf".
• Generate cDNA sequence FASTA ---> "-cw".
• Generate Reverse cDNA sequence FASTA ---> "-rcw".
• Generate mRNA sequence FASTA ---> "-tw".
• Calculate Codon Usage Bias(CUB) ---> "-cub".
• Export Codon Usage Bias(CUB) to CSV file ---> "-wcub".
• Calculate Hydrogen Bonds of dsDNA ---> "-hb".
• Caclulate the Genome coverage(x) ---> "-cx".
• Calculate FASTQ quality control ---> "-fqc".

More functions will be added in the future.

Note

If you have any suggestions for new features or a bug encountered, create an Issue or send me a message at: mikeph526@outlook.com. I'm happy to help.

Testing

Various tests have been performed to ensure scientific accuracy and the optimal computing performance. Everything involving unit testing can be found in this repository.

Examples

In order to test BioGenie functions, example files are provided in the sample fasta folder. In the table bellow, are all the necessary information about the said files.

Name	Description	NCBI Acc. Number
pst_dc3k.fa	Genome of P.syringae DC3000	ASM780v1
hopB1.fasta	Sequence of hopB1 gene	NC_004578.1
pgp_prot.faa	Protein sequence of Human PGP	NP_001035830.1
primer.fasta	A selection of well-known primers	Various
hemoglobin_pdec.fasta	P.decipiens gene for hemoglobin	Z11681.1
test.fastq	A fictional sequence to test FASTQ support	Fictional
pwa.fasta	A test file for PGSA testing	Fictional
pwa2.fasta	A test file for PLSA testing	Fictional

Installation

GNU Linux

• Download BioGenie from Releases, or with wget:

wget https://github.com/mikeph52/BioGenie/releases/download/v.1.2.0/biogenie_linux_1.2.2

• Run "chmod +x" first.

sudo chmod +x biogenie_linux_1.2.2

• Move it to bin folder by executing the following command:

sudo mv biogenie_linux_1.2.2 /usr/local/bin/biogenie

• If you need to build from source:

git clone https://github.com/mikeph52/BioGenie.git
clang++ main.cpp -o biogenie
sudo mv biogenie /usr/local/bin/

macOS

It supports Intel and Apple silicon processors.

• Download BioGenie from Releases, or with curl:

curl -l https://github.com/mikeph52/BioGenie/releases/download/v.1.2.2/biogenie_macos_1.2.2

• Run "chmod +x" first.

sudo chmod +x biogenie_macos_1.2.2

• Move it to bin folder by executing the following command:

sudo mv biogenie_macos_1.2.2 /usr/local/bin/biogenie

• If you need to build from source(probably not):

git clone https://github.com/mikeph52/BioGenie.git
clang++ -std=c++17 main.cpp -o biogenie
sudo mv biogenie /usr/local/bin/

MS Windows

Important

Windows is back(sort of). From version v.0.28.0, windows is supported. Still, this version is not going to be prioritized.

It requires Windows 10 or later.

• Download BioGenie from Releases or run:

wget.exe https://github.com/mikeph52/BioGenie/releases/download/v.1.2.2/biogenie_windows_1.2.2.exe

• Open Start and search for Environment Variables.
• Click Edit the system environment variables.
• In the System Properties window, click Environment Variables.
• Under User variables (for current user) or System variables (for all users), select Path and click Edit.
• Click New and paste the folder path where your biogenie .exe lives (for example C:\Bioinfo\CLI).
• Click OK on all open dialogs to save and close them.
• Close and reopen any Command Prompt/PowerShell windows so they pick up the updated PATH.

There's also a GUI Version Available on Alpha testing.

Caution

This is an Alpha testing version. It is not functional. Not for scientific use. I don't think it is possible to make and maintain a gui version for windows. The code is complicated already. It's time to move on.

Instal with conda

From version 1.1.0 BioGenie is available on conda, visit the conda page.

Note

Biogenie on conda currently supports only macOS-arm64. Support for multiple platforms will be released on the next update.

• Run this command:

conda install mikeph52::biogenie

• It is highly advisable to create a conda environment first:

conda create -n biogenie

Soon it will uploaded on bioconda.

Changelog:

1.2.2 (March 24th, 2026)

• Issue (#50) fixed.

1.2.0 (March 24th, 2026)

• Quality control for FASTQ files added.
• Conda support added.
• Minor bugs fixed.

1.1.0 (March 6th, 2026)

• Genome Coverage(x) added.
• Genome Coverage(x) added in "-asmbl" pipeline.
• FASTQ support added.
• FASTQ to FASTA function added.
• Major file-handling improvements made.
• Documentation enhanced.

1.0.0 (March 3rd, 2026)

• Issue (#42) fixed.
• Documentation enhanced.
• Minor bugs and formatting issues fixed.

For more info checkout the changelog.