This is a list of computer software which is made for bioinformatics and released under open-source software licenses with articles in Wikipedia.
- Sequence assembly - you don't need your own contig assembly program when you can use: EGassember - aligns and merges sequence fragments resulting from shotgun sequencing or gene transcripts (EST) fragments in order to reconstruct the original segment or gene (Reference: A. Masoudi-Nejad et al.
- CAP3 Assembly Program. A version of CAP3 for a 64-bit Linux system with an Intel processor: download tar file. This version can accept sequences of length = 30 kb; there is no need to specify this with an option. A version of CAP3 for a 32-bit Linux system with an Intel processor download tar file.
Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap. Finishing capabilities include allowing the user to pick primers and templates, suggesting additional sequencing reactions to perform, and facilitating checking the accuracy of the assembly using digest and forward/reverse pair information. Staden Package homepage. Introduction News; A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows. OrangeScrum is a free, open-source project management tool with a robust community that is always adding new features and add-ons for the software. OrangeScrum is a project management tool and not specifically a construction management tool, but unlike many project management tools it is geared toward the construction industry, among others.
| Software | Description | Platform | License | Developer |
|---|---|---|---|---|
| .NET Bio | Language-neutral toolkit built using the Microsoft 4.0 .NET Framework to help developers, researchers, and scientists | .NET Framework | Apache | Collaborative project |
| AMPHORA | Metagenomics analysis software | Linux | GPL | ? |
| Anduril | Component-based workflow framework for data analysis | Linux, macOS, Windows | GPL | University of Helsinki |
| Ascalaph Designer | Computer program for general purpose molecular modelling for molecular design and simulations. | ? | GPLv2 | Agile Molecule |
| AutoDock | Suite of automated docking tools | ? | GPL | ? |
| Avogadro | C++ (Qt) based molecule editor and visualizer for in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. | ? | GPL | ? |
| BEDtools | 'Genome arithmetic' -- manipulation of coordinate sets and the extraction of sequences from a BED file. | Linux | MIT | QuinlanLab, University of Utah |
| Bioclipse | Visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP) | ? | Eclipse Public | The Bioclipse Project |
| Bioconductor | R (programming language) language toolkit | Linux, macOS, Windows | Artistic 2.0 | Fred Hutchinson Cancer Research Center |
| BioJava | Java library functions for manipulating sequences, protein structures, file parsers, CORBA interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines | Linux, macOS, Windows | LGPL v2.1 | Open Bioinformatics Foundation |
| BioJS | JavaScript library of components to visualize biological data | Web browser | Apache | ? |
| BioMOBY | Registry of web services | Web browser | Artistic | Open Bioinformatics Foundation |
| BioPerl | Perl language toolkit | Cross-platform | Artistic, GPL | Open Bioinformatics Foundation |
| BioPHP | PHP language toolkit with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools | Cross-platform | GPL v2 | Open Bioinformatics Foundation |
| Biopython | Python language toolkit | Cross-platform | Biopython[1] | Open Bioinformatics Foundation |
| BioRuby | Ruby language toolkit | ? | GPL v2 or Ruby | Open Bioinformatics Foundation |
| BLAST | Algorithm and program for comparing primary biological sequence information, including DNA and protein sequences. | Cross-platform | Public domain | National Center for Biotechnology Information |
| CP2K | Perform atomistic simulations of solid state, liquid, molecular and biological systems, written in Fortran 2003. | ? | GPL and LGPL | Free open source GNU GPLv2 or later |
| EMBOSS | Suite of packages for sequencing, searching, etc. written in C | ? | GPL and LGPL | Collaborative project |
| Galaxy | Scientific workflow and data integration system | Unix-like | Academic Free | Collaborative project |
| GenePattern | Scientific workflow system that provides access to hundreds of genomic analysis tools | Unix-like (public server); Linux, macOS, Windows | MIT | Broad Institute, UC San Diego |
| Geworkbench | Genomic data integration platform | Linux, macOS, Windows | GeWorkbench License[2] | Columbia University |
| GMOD | Toolkit to address many common challenges at biological databases | Unix-like (server), Web browser (client) | Varies depending on tool | Collaborative project |
| GenGIS | Application that allows combining digital map data with information about biological sequences collected from the environment | Windows, macOS | GPL | Collaborative project |
| Genomespace | Centralized web application that provides data format transformations and facilitates connections with other bioinformatics tools | Web browser | LGPL | Broad Institute, collaborative project |
| GENtle | An equivalent to the proprietary Vector NTI, a tool to analyze and edit DNA sequence files | ? | GPL | Magnus Manske |
| GROMACS | Molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. | Linux, macOS, Windows | Common Public 1.0 | GenoViz |
| Integrated Genome Browser | Java-based desktop genome browser | Linux, macOS, Windows | Common Public 1.0 | GenoViz |
| InterMine | Extensive data warehouse system for the analysis and integration of biological datasets written in Java and JavaScript | Cross-platform | LGPL | University of Cambridge |
| LabKey Server | Software platform, allows organizations to integrate, analyze, and share complex biomedical data | Linux, macOS, Windows | Apache | LabKey Software Foundation |
| LAMMPS | Molecular dynamics program written in C++ | Linux, macOS, Windows | Apache | Sandia National Laboratories. |
| mothur | Software for analysis of the 16S rRNA gene | Linux, macOS, Windows | ? | University of Michigan |
| PathVisio | Desktop software for drawing, analyzing, and visualizing biological pathways | Linux, macOS, Windows | Apache 2.0 | Maastricht University |
| Orange | Component-based data mining and machine learning software suite written in C++, featuring a visual programming front-end for exploratory data analysis and interactive visualization, and Python bindings and libraries for scripting | Linux, macOS, Windows | GPL | University of Ljubljana |
| SAMtools | Utilities for interacting with high-throughput sequencing data and alignments in sam/bam format | Unix/Linux | MIT | Collaborative project |
| SOAP Suite | Suite of tools for assembly, alignment, and analysis of short read next generation sequencing data | Unix/Linux, macOS | GPL | BGI |
| Staden Package | Sequence assembly, editing, and analysis, mainly consisting of gap4, gap5, and spin. Written in C, C++, Fortran and Tcl. | Linux, macOS, Windows | BSD | Wellcome Trust Sanger Institute, Medical Research Council |
| Taverna workbench | Tool to design and execute workflows | Linux, macOS, Windows | LGPL | myGrid |
| UGENE | Integrated bioinformatics tools, written in C++ (Qt) | Linux, macOS, Windows | GPL 2 | Unipro |
| Unipept | Metaproteomics biodiversity analysis written in Ruby and JavaScript | Web browser | MIT | Ghent University |
| VOTCA | A Coarse-grained modeling package for molecular dynamics, written in C++, Perl, BASH | Linux, macOS, Windows, any other Unix variety | Apache License 2.0 | Max Planck Institute for Polymer Research |
See also[edit]
References[edit]
- ^Biopython License
- ^'GeWorkbench License'. geWorkbench. Columbia University. 15 June 2014.
External links[edit]
- Free Biology Software – Free Software Directory – Free Software Foundation
Cap3 Sequence Assembly Program Windows Apps
Retrieved from 'https://en.wikipedia.org/w/index.php?title=List_of_open-source_bioinformatics_software&oldid=1036345099'
Sanger Sequencing Analysis
- Improve your mapping accuracy and decrease your analysis time with simple sequence assembly and easy editing of contigs
- Automatic annotation for gene prediction, motifs, translation, and variant calling
- Genotype microsatellite traces with automated ladder fitting and peak calling and generate tables of alleles
Next Generation Sequencing Analysis
- Beautiful visualizations of annotated genomes and assemblies displayed in a highly customizable sequence view
- Powerful SNP variants analysis with your choice of algorithm or easy viewing of provided variant calls
- Simple RNA-Seq expression analysis without any expertise in the statistical programming language, R, needed
Molecular Biology
- Simulate a variety of molecular cloning operations in one step including restriction, Gateway, Golden Gate and In-Fusion cloning
- Design and test PCR and sequencing primers with the elegant primer design tool and create your own searchable primer database
- Powerful CRISPR tools make it quick and easy to find sites, design guide RNAs and analyze your editing results
NGS Pre-Processing, Assembly and Mapping
- Accurate downstream analysis with extensive NGS pre-processing tools producing clean sequence data
- Reliable reference mapping with exclusive mapping algorithms producing superior results
- Flexible de novo genome assembly can handle data from all sequencing machines with alignment tools available for comparison and finishing
Alignment and Phylogenetics
- Perform pairwise and multiple alignments of DNA or protein using trusted algorithms, including MAFFT and Clustal Omega
- Build phylogenetic trees using peer-reviewed algorithms, including RAxML and PAUP*, and adjust display settings for publication-ready graphics
NCBI and BLAST
- Rapidly search all key databases at NCBI for literature, DNA and protein sequence information or set up automated agents to do the searching for you
- BLAST search against sequences in NCBI databases with results returned directly into Geneious Prime or set up a local database and BLAST it locally
- Submit sequences directly to GenBank including genomes, features, primers traces and more
What’s New in Geneious Prime 2021.2?
- Updates include virtual gel improvements, viewing CRISPR cut sites, batch editing annotations and viewing invalid CDS annotations
- Discover all of the brand new features, improvements, and enhancements inGeneious Prime 2021.2
Data Management
Increase process efficiency and improve collaboration with intuitive folder-based organization and a seamlessly integrated shared database. Simple drag and drop for import and export of a large number of common file formats including GenBank, SnapGene and FASTQ.
Customization
Extend the functionality of Geneious Prime with our collection of plugins available for assembly, alignment, phylogenetics and more. Integrate with existing systems and add your own custom algorithms using a highly interoperable API.
Automation
Create your own automated workflows or use in-built workflows to increase efficiency and reduce human error. Automate external database searches to continuously receive the latest information on genomes, sequences, and protein structures.
Innovation
We care a great deal about finding new ways to get science done faster and more efficiently. Our development team works constantly throughout the year to ensure Geneious Prime runs beautifully and there’s always a new release around the corner.
Geneious is an absolutely beautiful package to work with. We love it and we are telling everyone about it.
Geneious cannot be overestimated! A (work) life without Geneious is no longer possible – it feels dark, cold and hostile…
Viral Vector Facility (VVF) of the Neuroscience Center Zurich (ZNZ)
Geneious has done a great deal for our lab, and I think it adds incredible value for labs with a mixture of wet and dry folks or those doing lots of cloning like ours.
I find that Geneious is more than an invaluable tool for any modern molecular lab, it is an engine by itself that drives all our research and speeds up design, strategy and innovation.
Dept. of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Israel
Geneious is the perfect combination of ease-of-use and bioinformatic refinement.
Plant and Wildlife Science Dept. Brigham Young University
Explore a list of the comprehensive set of molecular biology and sequence analysis tools available in Geneious Prime
NGS Pre-Processing
- Import Illumina, PacBio and NanoPore reads
- Trim, filter and demultiplex both single-end and paired-end data
- Merge paired reads
- De-duplicate
- Error correct and normalize
- Filter out chimeras
Mapping and de novo Assembly
- Simply switch between industry leading algorithms for mapping and de novo assembly
- Support for assembly of Sanger and NGS data, including Illumina, PacBio and Oxford Nanopore reads of any length, including paired-end reads and hybrid assemblies
- Produce circular contigs when assembling microbial genomes, plasmids and other circular sequences
- Genome comparison and finishing with MAUVE genome alignment
- Mappers including Geneious, Geneious for RNA Seq, BBMap, Minimap2, Bowtie2 and TopHat
- De novo assembly algorithms including Geneious, SPAdes, Flye, MIRA, Tadpole and Velvet
Variant Calling and Expression Analysis
- Call SNPs/variants using Geneious or FreeBayes
- Perform real-time filtering of tabular results with synchronized genome view
- Calculate and compare expression levels on mapped RNA-seq data
- Visualize using PCA and volcano plots
Sequence Analysis
- Trim, assemble, and view Sanger sequencing trace files
- Correct base calls and create consensus sequences
- Annotate motifs, ORFs and repeats
- Predict genes and structural elements
- Real-time annotation via similarity search against database
- Translate selections on the fly, or show translation for annotations or selected frame
- Dynamic graphs and statistics for sequence properties such as pI, molecular weight, melting point, AA composition and more
Sequence Alignment
- Multiple and pairwise sequence alignment of DNA or protein including full genome alignment
- Align with trusted algorithms including Geneious Aligner, MUSCLE, MAFFT, Clustal Omega, MAUVE and LastZ
- View and edit alignments with real-time translation and highlighting
Phylogenetics
- Build trees with Geneious tree builder, MrBayes, PAUP*, PhyML, RAxML and more
- Visualize, edit and markup your trees
- Interactive distance matrix viewer
- Publication quality export
Microsatellite Analysis
- Import raw ABI trace files
- Trim, predict and manually adjust peaks
- Bin peaks into alleles
- Produce tabular output of allele calls
Molecular Cloning
- View plasmid maps, automatically annotate vectors, and copy-paste sequences with annotations
- One-step GoldenGate (Type IIS) and Restriction cloning
- Homology-based cloning including Gibson, GeneArt, and In-Fusion
- TOPO cloning
- Parent/descendant lineage tracking of cloning operations
- Codon optimization and back translation
- Silent mutation analysis to find potential restriction sites to introduce
- Simulated PCR, digestion and ligation
Primer Design
- Automatically design PCR and sequencing primers and hybridization probes, to any target region or entire sequence
- Easily add primers in the Sequence View
- Design basic and degenerate PCR primers
- Add and remove extensions to a primer sequence before, during or after the design process
- Primer specificity testing to check for additional binding sites on the template sequence
- Screen for physical properties, hairpins and primer-dimers
- Drag and drop your primers in FASTA, spreadsheet or GenBank format
Cap3 Sequence Assembly Program Windows Apps Free
Data Management and Collaboration
- Drag and drop import of files and folders, including Vector NTI databases
- Import metadata from a spreadsheet onto sequences and other documents
- Smart NGS import – one step import of any assortment of SAM, BAM, GFF, BED, and VCF files
- Intuitive folder-based project organization
- Seamlessly integrated shared database
- Rapid search against all sequences and metadata in your database
- Extensive export options
Searching and BLAST
- Direct access to NCBI public BLAST databases
- Custom BLAST for private local databases
- Integrated search of external databases including GenBank and UniProt
- Upload your sequences directly to GenBank
- Search for literature in PubMed
- Advanced searching against your local or shared database
Automated Workflows
- Create workflows for automated bulk analysis using a visual editor
- More than 20 in-built workflows for performing pipelines including Apply Variants to Reference Sequence, Map Reads then find SNPs, and Randomly Sample Sequences
- Extend capabilities with option to write custom code workflows
API & Developers
- Add specialized functionality or integrate with other systems using the Plugin Development Kit
- Add your favorite algorithm, database or visualization
- Wrap a command line program to run via the Geneious Prime GUI
Discover how Geneious tools and services can help you simplify and empower sequencing research and analysis.