Search Results for "bioinformatics"
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Showing 409 open source projects for "bioinformatics"
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Bowtie 2
A fast and sensitive gapped read aligner
...The tool builds compact FM-index-based reference indexes, keeping memory usage low even for large genomes like the human genome. Bowtie 2 outputs alignments in SAM format and includes companion utilities for building and inspecting indexes. It is widely used in bioinformatics pipelines for RNA-seq, DNA-seq, metagenomics, variant analysis, and other sequencing-based research tasks. Overall, Bowtie 2 remains a foundational command-line tool for high-throughput sequence alignment and reproducible computational biology workflows. -
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Volcano
A Cloud Native Batch System (Project under CNCF)
Volcano is a batch system built on Kubernetes. It provides a suite of mechanisms that are commonly required by many classes of batch & elastic workload including machine learning/deep learning, bioinformatics/genomics, and other "big data" applications. These types of applications typically run on generalized domain frameworks like TensorFlow, Spark, Ray, PyTorch, MPI, etc, which Volcano integrates with. Volcano builds upon a decade and a half of experience running a wide variety of high-performance workloads at scale using several systems and platforms, combined with best-of-breed ideas and practices from the open-source community. ... -
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Prokka
Rapid prokaryotic genome annotation
Prokka is a command-line software tool for rapid annotation of prokaryotic genomes (bacteria and archaea). Given a FASTA file of contigs, it predicts genes, rRNAs, tRNAs, and other functional elements, then assigns functions by comparing to reference protein databases and HMM profiles. It outputs GenBank, GFF, and other formats compatible with downstream tools and genome browsers. Prokka handles common complications—overlapping ORFs, frameshifts, alternate start codons—while providing... -
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nextflow
A DSL for data-driven computational pipelines
Nextflow is a powerful workflow orchestration tool designed for the development and execution of data-intensive pipelines, especially in the field of bioinformatics. It enables reproducible and portable workflows that can run seamlessly across different environments including local, HPC clusters, and cloud platforms. With support for containers and software package managers, Nextflow makes it easy to define complex data processes using a concise DSL and manage dependencies efficiently. -
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Codon
A high-performance, zero-overhead, extensible Python compiler
...The Codon framework is fully modular and extensible, allowing for the seamless integration of new modules, compiler optimizations, domain-specific languages and so on. We actively develop Codon extensions for a number of domains such as bioinformatics and quantitative finance. -
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AlphaFold 3
AlphaFold 3 inference pipeline
...This repository provides the complete inference pipeline for running AlphaFold 3, though access to the model parameters is restricted and must be obtained directly from Google under specific terms of use. The system is designed for scientific research applications in structural biology, biochemistry, and bioinformatics, enabling accurate modeling of proteins, ligands, and covalent modifications. Users can perform local predictions via Docker containers, integrating AlphaFold 3’s inference process with provided JSON input configurations. The software includes flexible options for running both data preprocessing and GPU-accelerated inference, allowing users to adapt to available computational resources. -
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MedgeClaw
Open-source AI research assistant for biomedicine
MedgeClaw is a specialized AI-powered research assistant tailored for biomedical and scientific workflows, built on top of OpenClaw and Claude Code architectures. It integrates a large library of domain-specific skills, enabling it to perform complex analyses in areas such as genomics, drug discovery, and clinical research. The system connects conversational interfaces with computational environments, allowing users to initiate research tasks through messaging platforms while the backend... -
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DGL
Python package built to ease deep learning on graph
...Scale to giant graphs via multi-GPU acceleration and distributed training infrastructure. DGL empowers a variety of domain-specific projects including DGL-KE for learning large-scale knowledge graph embeddings, DGL-LifeSci for bioinformatics and cheminformatics, and many others. We are keen to bringing graphs closer to deep learning researchers. We want to make it easy to implement graph neural networks model family. We also want to make the combination of graph based modules and tensor based modules (PyTorch or MXNet) as smooth as possible. DGL provides a powerful graph object that can reside on either CPU or GPU. ... -
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...Especially, it supports whole genome sequencing data even with low sequencing depth. If you use Lep-MAP3, please cite P. Rastas. Lep-MAP3: Robust linkage mapping even for low-coverage whole genome sequencing data, Bioinformatics. 2017, 33(23):3726-3732. https://doi.org/10.1093/bioinformatics/btx494. Please note Lep-Anchor for anchoring genomes with Lep-MAP3 linkage maps http://sourceforge.net/projects/lep-anchor
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Lep-Anchor
Linkage map guided genome anchoring
Lep-Anchor has been developed to efficiently anchor genomes into chromosomes by using all the information provided by Lep-MAP3 and the additional information provided by long reads and contig-contig alignments to link contigs and to collapse haplotypes. Lep-Anchor supports millions of markers over multiple maps. Pasi Rastas, Lep-Anchor: Automated construction of linkage map anchored haploid genomes, Bioinformatics, btz978, https://doi.org/10.1093/bioinformatics/btz978 -
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Armadillo
fast C++ library for linear algebra & scientific computing
* Fast C++ library for linear algebra (matrix maths) and scientific computing * Easy to use functions and syntax, deliberately similar to Matlab / Octave * Uses template meta-programming techniques to increase efficiency * Provides user-friendly wrappers for OpenBLAS, Intel MKL, LAPACK, ATLAS, ARPACK, SuperLU and FFTW libraries * Useful for machine learning, pattern recognition, signal processing, bioinformatics, statistics, finance, etc. * Downloads: http://arma.sourceforge.net/download.html * Documentation: http://arma.sourceforge.net/docs.html * Bug reports: http://arma.sourceforge.net/faq.html * Git repo: https://gitlab.com/conradsnicta/armadillo-code -
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CpGtools
Python package to analyze DNA methylation data
CpGtools package provides a number of Python programs to annotate, QC, visualize, and analyze DNA methylation data generated from Illumina HumanMethylation450 BeadChip (450K) / MethylationEPIC BeadChip (850K) array or RRBS / WGBS. -
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Fastq-Fasta Converter
A bioinformatics tool that converts Fastq into Fasta
Fastq-Fasta Converter is a desktop application that converts Fastq files into Fasta files. -
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...Citation: Ma, Y.F., Yin, G.H., Pan, Y., and Liu, Y. (2026). Intelligent antigen design combined with yeast display enhances targeted immune responses. Briefings in Bioinformatics 27, bbag393.
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CpDB tutorial
Hands-on automatic annotation tutorial in Linux
This tutorial was conceived for a five hours course teaching automatic annotation to students with basic Linux OS concepts and some bioinformatics background. This is part of a book chapter available at the address https://doi.org/10.5772/23724. This is an alternative mirror for the site presented in the book chapter, a site no longer available. The parser's source code is available at sourceforge.net/projects/cpdb/. -
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Avogadro
An intuitive molecular editor and visualization tool
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture. -
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Bandicoot
fast C++ library for GPU linear algebra & scientific computing
* Fast GPU linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use * Provides high-level syntax and functionality deliberately similar to Matlab * Provides an API that is aiming to be compatible with Armadillo for easy transition between CPU and GPU linear algebra code * Useful for algorithm development directly in C++, or quick conversion of research code into production environments * Distributed under the permissive Apache 2.0 license, useful for both open-source and proprietary (closed-source) software * Can be used for machine learning, pattern recognition, computer vision, signal processing, bioinformatics, statistics, finance, etc * Downloads: http://coot.sourceforge.io/download.html * Documentation: http://coot.sourceforge.io/docs.html * Bug reports: http://coot.sourceforge.io/faq.html * Git repo: https://gitlab.com/conradsnicta/bandicoot-code -
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QUAST
Quality Assessment Tool for Genome Assemblies
...The tool also produces web-based reports condensing all information in one easy-to-navigate file. QUAST and its three follow-up papers (MetaQUAST, Icarus, QUAST-LG) papers were published in Bioinformatics; the last paper (WebQUAST) is out in Nucl Acid Research. -
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MetRFinder
Detection of Heavy Metal Resistance Genes from Bacterial Proteomes
MetRFinder is a standalone GUI-based bioinformatics tool developed in Python for rapid identification of heavy metal resistance genes from bacterial proteomes. The software integrates DIAMOND BLASTP with BacMet Experimental and BacMet Predicted databases to enable high-throughput screening of protein FASTA files. Users can analyze single or multiple bacterial isolates through an intuitive graphical interface without requiring command-line expertise. -
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CemCon
Automated SMILES-to-optimized 3D molecular structure converter
...The software is designed to simplify ligand preparation workflows for molecular docking, virtual screening, molecular dynamics simulations, and other Computer-Aided Drug Design (CADD) applications. Developed by Abhijit Reang and Sandip Das under the supervision of Dr. Arabinda Ghosh, Department of Molecular Biology and Bioinformatics, Tripura University, India. © 2026 -
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DataPrep
Python-based data preprocessing tool
DataPrep v0.2 is a Tkinter-based GUI application/tool designed to assist users in data preprocessing, multicollinearity removal, and feature selection for a wide range of applications in Cheminformatics, Bioinformatics, Data Analysis, Feature Selection, Molecular Modeling, Machine Learning, and Quantitative-structure-property relationship (QSPR) studies. It includes functionality to load, process, and save datasets with support for different preprocessing & multicollinearity removal strategies with customizable parameter setting options. -
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UniversalMer
A CLI k-mer counting tool for multiple sizes of k at once.
...The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists. -
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OligoYap Portable
Oligo design and bioinformatic analysis software.
OligoYap can be used to design classical PCR, SYBR Green, TaqMan, MGB, Molecular Beacons, Microarray and Real-Time PCR primers/probes and for bioinformatics analysis. It has the features of enzyme cut analysis, mutation analysis, DNA/protein match and BLAST. You can easily record laboratory materials/files, prepare PCR mix and many other laboratory operations. It works on windows8.1 and earlier operating systems, but has not been tried on windows10 and later. For better images, you can right-click the exe file and check the features/compatibility "Disable screen scaling in high DPI settings" box. ... -
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AngClust
AngClust: Angle-based feature clustering for time series
Citation: Aimin Li, Siqi Xiong, Junhuai Li, Saurav Mallik, Yajun Liu, Rong Fei, Hongfang Zhou, Guangming Liu. AngClust: Angle Feature-Based Clustering for Short Time Series Gene Expression Profiles. January 2022. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM. DOI: 10.1109/TCBB.2022.3192306 Full text: https://ieeexplore.ieee.org/document/9833353/ https://pubmed.ncbi.nlm.nih.gov/35853049/ Highlights * We proposed a novel clustering algorithm based on angular features for short-term gene expression profiles. * We defined three indicators to identify significant clusters: (i) the fluctuation degree of expression levels, (ii) homogeneity, and (iii) the degree of clustering while the clusters are functionally significant... -
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CpDB
Relational database schema and tools for bacterial genome annotation
...Besides the database, there is software, like a parser, to convert EMBL or GBK files to the CpDB relational schema. Once in the CpDB, one can extract unlimited reports from bacterial genomes using SQL. This software is part of the Ph.D. in Bioinformatics from Anderson Santos (https://orcid.org/0000-0003-3418-0823) developed under the Corynebacterium pseudotuberculosis (Cp) pangenome project. The Cp pangenome delivered to the scientific community fifteen bacterial strains deposited at the GenBank database between the years of 2009 and 2012. The thesis was written in Brazilian Portuguese. ...
