Open Source Unix Shell Bio-Informatics Software
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Unix Shell Bio-Informatics Software
View 64 business solutionsBrowse free open source Unix Shell Bio-Informatics Software and projects below. Use the toggles on the left to filter open source Unix Shell Bio-Informatics Software by OS, license, language, programming language, and project status.
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Gen AI apps are built with MongoDB AtlasMongoDB Atlas is the developer-friendly database used to build, scale, and run gen AI and LLM-powered apps—without needing a separate vector database. Atlas offers built-in vector search, global availability across 115+ regions, and flexible document modeling. Start building AI apps faster, all in one place.
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Peer to Peer Recognition Brings Teams TogetherCreate a positive and energetic workplace environment with Motivosity, an innovative employee recognition and engagement platform. With Motivosity, employees can give each other small monetary bonuses for doing great things, promoting trust, collaboration, and appreciation in the workplace. The software solution comes with features such as an open-currency open-reward system, insights and analytics, dynamic organization chart, award programs, milestones, and more.
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MitoSAlt
Identification of mitochondrial structural alterations
MitoSAlt is a pipeline to identify large deletions and duplications in human and mouse mitochondrial genomes from next generation whole genome/exome sequencing data. The pipeline is capable of analyzing any circular genome in principle, as long as a proper configuration file is provided. -
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MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome variability and disease-associations for mitochondrial variants. MToolBox provides also a Variant Call Format file (version 4.0) featuring, for the first time, allele-specific heteroplasmy. Please, check out the most recent updates of the source code with the Github repository of MToolBox: https://github.com/mitoNGS/MToolBox or visit the Web version of MToolBox @ MSeqDR: https://mseqdr.org/mtoolbox.php -
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cnvOffSeq
detecting & genotyping intergenic CNVs using off-target exome data
cnvOffSeq is a set of Java-based command-line tools for detecting and genotyping intergenic copy number variation (CNV) using off-target data from whole-exome sequencing experiments. -
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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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Attack Surface Management | Criminal IP ASMCriminal IP’s Attack Surface Management (ASM) is a threat-intelligence–driven platform that continuously discovers, inventories, and monitors every internet-connected asset associated with an organization, including shadow and forgotten resources, so teams see their true external footprint from an attacker’s perspective. The solution combines automated asset discovery with OSINT techniques, AI enrichment and advanced threat intelligence to surface exposed hosts, domains, cloud services, IoT endpoints and other Internet-facing vectors, capture evidence (screenshots and metadata), and correlate findings to known exploitability and attacker tradecraft. ASM prioritizes exposures by business context and risk, highlights vulnerable components and misconfigurations, and provides real-time alerts and dashboards to speed investigation and remediation.
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Tool for metagenomic viral community profiling
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MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection
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ProtPOS
Prediction of PROTtein Preferred Orientation on a Surface
ProtPOS is a self-contained, lightweight, and easy-to-use software package for predicting the preferred orientation of protein on a given surface upon initial adsorption. It searches quickly for the low energy protein poses in all translational and rotational degrees of freedom of the protein with respect to the surface using particle swarm optimization. Each successful run returns the lowest energy orientation of the protein on the surface in PDB format, which is readily used for MD simulations. ProtPOS is implemented in Python, making use of the PyMOL library for generating protein conformations and calling GROMACS externally to calculate protein-surface interaction energies. https://cbbio.online/software/protpos/ -
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ADOMA stands for: Alternative Display Of Multiple Alignment. ADOMA can create four different displays of a multiple sequence alignment: a ClustalW alignment in HTML format, a simplified ClustalW alignment in HTML and/or txt format and a colored ClustalW alignment in HTML format. For examples of these outputfiles check the screenshots. ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW. ADOMA is a commandline program that can easily be used in pipelines. For more information check the README.md in the Files section. How to cite ADOMA: Zaal, D. and Nota, B. (2016), ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output. Mol. Inf., 35: 42–44. doi: 10.1002/minf.201500083 http://onlinelibrary.wiley.com/doi/10.1002/minf.201500083/abstract
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ALEXA-Seq is a method for using massively parallel paired-end transcriptome sequencing for 'alternative expression analysis'.
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Combine Jira and SCM data to improve team performanceJellyfish is the leading Engineering Management Platform, providing complete visibility into engineering organizations, the work they do, and how they operate. By analyzing engineering signals from Git and Jira, qualitative team feedback, and contextual business data from roadmapping, incident response, HR, calendar, and collaboration tools, Jellyfish enables engineering leaders to align engineering decisions with business initiatives and deliver the right software, efficiently, on time. With Jellyfish, engineering leaders can focus their teams on what matters most to the business, driving strategic decisions and delivering results.
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Amplicon_Sequencing_Worfklow
Analyzing amplicon data from sequences to stats
This is a collection of scripts and instructions on how to analyzing amplicon sequence data (i.e., 16S, ITS2, & other marker genes). I created this workflow to create a consistent set of methods for analyzing amplicon sequence data, from when you first receive the sequence data to statistical analyses & data visualization. All you need is to have the latest version of R installed, some experience with the command line & shell, and enough memory to run all of the programs. There are also instructions provided in case you are running these analyses via a computing cluster/Slurm workload manager. You can choose to go through the workflow using either an Rmd script, an html file, or a PDF, or via the homepage link provided. If you have questions or concerns, please don't hesitate to reach out. Thanks! -
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ArrayOligoSelector (AOS) systematically designs gene specific long oligo probes for entire genomes. The program optimizes the oligo selections for several parameters, including uniqueness in the genome, internal repeats, self-binding, and GC content.
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Tools to build molecular-docking activity prediction models by PLS regression with iterative training and pose-selection. Descriptors include (i) docking score(s), (ii) pharmacophore features, (iii) multi-feature descriptors learned by decision trees.
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BCAR is a library for the associative classification, which denotes "Boosting Class Association Rules". BCAR provides a general tool for classification tasks with various types of input data.
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Biospha is a suite of perl scripts based on bioperl toolkit intended to help researches to manage large sequence file. With BIOSPHA you can classify each sequence according to the NCBI taxonomy. You also can get all taxonomic info from a GI or Taxid.
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BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models presented are annotated and linked to relevant data resources and are available in various format
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A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.
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ChIP-RNA-seqPRO
ChIP-RNA-sequencing-processing (ChIP-RNA-seqPRO)
ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites. Runnable python scripts packaged together with customized annotation libraries, demo data input and README guide. 9/26 : v1.1 Updated MAIN_IV to debug error thrown by python pandas no longer supporting 'subset'. This code will no longer be actively maintained/updated here. A cloud-based resource for comparative analysis of epigenetic, sequence variation, and expression datasets is now available. Please visit the Cloudomics, project for cloud-based resources: https://sourceforge.net/projects/cloudomics-for-aws/ -
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CoDeCZ
Derive copy number status from targeted sequencing data
CoDeCZ derives copy number state from targeted sequencing data on gene or exon level. Results are NOT true copy number however, but they are semi-quantitative: It uses the modified z-score to calculate deviation in normalized coverage per specified region. The higher the Z-score, the higher the copy number. The final z-score depends on the quality of the data and the makeup of the reference pool. -
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ExonFinder
A pipeline to extract novel cassette exons/retained-introns
ExonFinder provides a pipeline to extract novel cassette exons and novel retained-introns from the results of mapping cross-species ESTs against a target genome via blat. -
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FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.
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Fast Neurite Tracer
Semi-automatic neurite tracing with tera-bytes of imaging data.
Fast Neurite Tracer (FNT) is a tool for semi-automated neurite tracing. FNT can handle big imaging data such as fMOST data. It can also process other types of light imaging data in general. FNT is designed to be * accurate in tracing (each tracing step needs your confirmation), * fast (operations using computer mouse is reduced with automatic searching), * scalable (large volume data of tera-bytes in size are supported). Other features include * the results can be exported to SWC files, * automatic detection of cycles during tracing, * support for data of multiple channels, * support for both 8-bit and 16-bit image data. -
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A Folding@Home integrated monitoring environment, designed for Linux, *nix systems and Windows, which is intended to be easy-to-use and provide a flexible, customiseable and "user-friendly" environment for reviewing the status of active F@H clients.
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The High Throughput Sequence Analysis Pipeline uses freely available bioinformatics tools from NCBI, Phylip, EMBOSS and clustalw to identify and group closely related DNA samples. It can be run on *Nix systems linearly or in parallel using the SGE.