Open Source C++ Bio-Informatics Software
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C++ Bio-Informatics Software
View 66 business solutionsBrowse free open source C++ Bio-Informatics Software and projects below. Use the toggles on the left to filter open source C++ Bio-Informatics Software by OS, license, language, programming language, and project status.
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Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
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The SourceForge OpenRasMol project is an adjunct to the RasMol and OpenrasMol project at http://rasmol.org. It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions.
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Free DELTA
Software tools for processing taxonomic descriptions in DELTA format
The Free DELTA Project is a free, open-source, software alternative for a generic system to the processing of taxonomic descriptions based on the DELTA (DEscription Language for TAxonomy) format. -
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MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.
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8 Monitoring Tools in One APM. Install in 5 Minutes.AppSignal works out of the box for Ruby, Elixir, Node.js, Python, and more. 30-day free trial, no credit card required.
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Systems Biology Markup Language (SBML)
A file format for exchanging computational models in systems biology
The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more. -
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skewer
A fast and sensitive adapter trimmer for illumina paired-end sequences
This program implements a novel dynamic programming algorithm dedicated to the task of adapter trimming and it is specially designed for processing illumina paired-end sequences. -
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This project, initially developed at University College London, contains programs to perform rigid, affine and non-linear registration of nifti or analyse images. Two versions of the algorithms are included, a CPU- and a GPU- (using CUDA) based implementation.
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A set of tools for working with VCF files, such as those generated by the 1000 Genomes Project. This project is migrating to github: https://vcftools.github.io/
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RasTop is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules based on the popular Rasmol software. The program is aimed at the rapid visualization and analysis of molecules.
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AI-generated apps that pass security reviewRetool lets you generate dashboards, admin panels, and workflows directly on your data. Type something like “Build me a revenue dashboard on my Stripe data” and get a working app with security, permissions, and compliance built in from day one. Whether on our cloud or self-hosted, create the internal software your team needs without compromising enterprise standards or control.
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MIRA V5 is available only on GitHub! The V4 version released here on SourceForge stay up as some automated release fetching packages rely on V4. MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.
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AMOS
AMOS is a collection of tools for genome assembly
AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation. -
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TinkerCell is a software for synthetic biology. The visual interface allows users to design networks using various biological "parts". Models can include modules and multiple cells. Users can program new functions using C or Python. www.tinkercell.
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Celera Assembler (CA) is a whole-genome shotgun (WGS) assembler for the reconstruction of genomic DNA sequence from WGS sequencing data.
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A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
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CBFLIB is a library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for mmCIF files.
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Maq is a set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.
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BLESS: NGS Error Correction Tool
Bloom-filter-based Error Correction Tool for NGS reads
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provean
Predicting the functional effect of protein sequence variations
PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. The prediction is based on the change, caused by a variation, in the similarity of query sequence to closely related sequences collected through BLAST. -
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CaspLab - Comet Assay Software Project Lab is a cross-platform image analysis software to measure level of DNA damage in SCGE (Single Cell Gel Electrophoresis) method called also comet assay method.
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PANDA
A comprehensive and flexible quantification tool for proteomics data
PANDA is a comprehensive and flexib tool for quantitative proteomics data analysis, which is developed based on our solid foundations in quantitative proteomics for years. Several novelties have been implemented in it. First, we implement the advantage algorithms of LFQuant (Proteomics 2012, 12, (23-24), 3475-84) and SILVER (Bioinformatics 2014, 30, (4), 586-7) into PANDA. Second, we consider the state-of-art concept of quantification reliability in this quantitative workflow. On the levels of spectra, peptides and proteins, PANDA works out a few quantitative filters and new scores for quantification confidence. Third, PANDA is designed for processing proteomics big data in parallel. -
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GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.
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scalpel
Genetic variants discovery tool
Bioinformatics pipeline for discovery of genetic variants from NGS reads. -
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Critterding
Evolving Artificial Life
Critterding is a "Petri dish" universe in 3D that demonstrates evolving artificial life. Critters start out with completely random brains and bodies, but will automatically start evolving into something with much better survival skills. -
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An open source framework for LC-MS based proteomics and metabolomics. OpenMS offers data structures and algorithms for the processing of mass spectrometry data. The library is written in C++. Our source code and wiki lives on GitHub (https://github.com/OpenMS/OpenMS).
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PhysiCell
physics-based multicellular simulator
PhysiCell is a cross-platform C++ framework for large, physics-based multicellular simulations.
