List of open-source bioinformatics software

SoftwareDescriptionPlatformLicenseDeveloper.NET BioLanguage-neutral toolkit built using the Microsoft 4.0 .NET Framework to help developers, researchers, and scientists.NET FrameworkApacheCollaborative projectAMPHORAMetagenomics analysis softwareLinuxGPL? Ascalaph DesignerComputer program for general purpose molecular modelling for molecular design and simulations.?GPLv2Agile MoleculeAutoDockSuite of automated docking tools?GPL?AvogadroC++ (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.LinuxMITQuinlanLab, University of UtahBioclipseVisual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP)?Eclipse PublicThe Bioclipse Project BioJavaJava library functions for manipulating sequences, protein structures, file parsers, CORBA interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routinesLinux, macOS, WindowsLGPL v2.1Open Bioinformatics FoundationBioJSJavaScript library of components to visualize biological dataWeb browserApache? BioPHPPHP language toolkit with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics toolsCross-platformGPL v2Open Bioinformatics Foundation CP2KPerform atomistic simulations of solid state, liquid, molecular and biological systems, written in Fortran 2003.?GPL and LGPLFree open source GNU GPLv2 or laterEMBOSSSuite of packages for sequencing, searching, etc. written in C?GPL and LGPLCollaborative project GMODToolkit to address many common challenges at biological databasesUnix-like (server), Web browser (client)Varies depending on toolCollaborative projectGenGISApplication that allows combining digital map data with information about biological sequences collected from the environmentWindows, macOSGPLCollaborative projectGenomespaceCentralized web application that provides data format transformations and facilitates connections with other bioinformatics toolsWeb browserLGPLBroad Institute, collaborative projectGENtleAn equivalent to the proprietary Vector NTI, a tool to analyze and edit DNA sequence files?GPLMagnus ManskeGROMACSMolecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids.Linux, macOS, WindowsCommon Public 1.0GenoViz InterMineExtensive data warehouse system for the analysis and integration of biological datasets written in Java and JavaScriptCross-platformLGPLUniversity of CambridgeLabKey ServerSoftware platform, allows organizations to integrate, analyze, and share complex biomedical dataLinux, macOS, WindowsApacheLabKey Software FoundationLAMMPSMolecular dynamics program written in C++Linux, macOS, WindowsApacheSandia National Laboratories. PathVisioDesktop software for drawing, analyzing, and visualizing biological pathwaysLinux, macOS, WindowsApache 2.0Maastricht University SAMtoolsUtilities for interacting with high-throughput sequencing data and alignments in sam/bam formatUnix/LinuxMITCollaborative project Taverna workbenchTool to design and execute workflowsLinux, macOS, WindowsLGPLmyGrid UGENEIntegrated bioinformatics tools, written in C++ (Qt)Linux, macOS, WindowsGPL 2UniproUnipeptMetaproteomics biodiversity analysis written in Ruby and JavaScriptWeb browserMITGhent UniversityVOTCAA Coarse-grained modeling package for molecular dynamics, written in C++, Perl, BASHLinux, macOS, Windows, any other Unix varietyApache License 2.0Max Planck Institute for Polymer Research

India started genomic surveillance early this year to study the mutating nature of COVID-19. The surveillance strategy is aimed at performing genome sequencing as a quick response measure. And bioinformatics tools have come to the rescue here founder taking such genomic test.

What is Genomic Testing?

Genomic testing is performed to study mutations ina gene. Mutations indicate the presence of disorders and diseases, sometimes asdeadly as cancer. Genomic sequencing tests identify differing levels ofexpression in a group of genes to understand their interactions. Test genomicanalysis is thus critical for understanding the activity of genes and making anaccurate prognosis.

What are the Different Types of Genomic Testing?

Genomic tests are a kind of medical tests done to rule out the possibility of a person having or developing a medical condition. These types of genomic testing are performed by geneticist or genetic counsellors:

  • Diagnostic testing

    Diagnostic testing is used for identifying genetic conditions that an individual may have. These are based on clinical presentations prepared by clinicians to confirm an initial diagnosis.

    This kind of genomic test is done by checking an allele or a specific gene variant associated with a particular kind of disease. Bioinformatics tools here help with sequencing the genomes for further analysis.

  • Clinical predictive testing

    Clinical predictive kind of genomic testing is done to see if or not an individual is susceptible to a certain disorder. Open source and free bioinformatics tools here help with examining the causative gene variant for targeted tests.

  • Pharmacogenomic testing

    Open source and free bioinformatics tools for Linux help with pharmacogenomic testing by studying the genomic determinants of different drug responses. This test genomic analysis helps assess whether a particular medicine would be effective.

  • Tumour testing

    Tumour testing helps with sequencing of DNAs to study the mutations within them. Bioinformatics tools are deployed here to do tumour testing. This type of genomic testing is quite important when it comes to diagnosing cancers and tumours.

Advances in Genomic Testing to Analyse Health Risks

Genome-wideanalysis and testing is critical for testing, monitoring and preventingdiseases across populations.

Next generation genome sequencing technologyundertakes parallel sequencing of DNA fragments for an efficient genomicanalysis. These tests are performed using samples of hair, blood, tissue,amniotic fluid or skin. Some of the most advanced methods today for genomictesting are:

  • Moleculartests for studying short length DNAs or single genes to examine mutations thatmay lead to genetic diseases.
  • Biochemicaltest studies the activity level or number of proteins. Any abnormality hereindicates the possibility of a genetic disorder.

Genomic testing has evolved newer advanced methods for analyzing the different health risks in new born. This is one area where genomic testing and medicine has advanced well and let us have a look here how:

  • Presymptomatic & predictive testing

    Presymptomatic & predictive testing is used in conditions where members of a family suffer from any kind of genetic disorder. This kind of genomic testing studies gene mutations to identify defects that may emerge either after birth or during later stages in life.

    One good example could be identifying certain types of cancers using presymptomatic & predictive type of genomic testing.

  • Carrier testing

    People with increased risk of suffering from a genetic disorder are administered this type of genomic testing. Carrier testing assesses people who have more than one copy of genetic mutation.

  • Prenatal testing

    Prenatal kind of test screens a foetus for changes in her or his chromosomes/genes. The process makes it possible to ensure whether the child would have any genetic disorder.

  • Chromosomal tests

    Chromosomal tests analyze long length DNAs and whole chromosomes to find out if there are massive genetic changes.

How Bioinformatics Tools Help with Genomic Testing

Bioinformatics software solutions areideal for genomic testing or next-generation sequencing. Next-generationsequencing technology is used to study mutations in genes for predictingthe nature of a disease.  

Ifwe speak about this technology in the Indian context, you would find that Indiahas started genome sequencing of COVID-19 using bioinformatics tools. Covid-19has protein binding on its membrane and is primarily an RNA virus. It isbecause of these components that the virus has acquired the character it hasand is fast mutating.

Howbiometric tools work is theydo genome sequencingtostudy the arrangement of DNA, RNA, and proteins in the virus to understand itschanging nature. Bioinformatics tools with their next generation sequencing andgenomic testing capabilities have been deployed by scientists in India thus tostudy such mutations.

Popular bioinformatics software solutions providecomputation infrastructure for genomic data analysis.Bioinformaticstools are thus based on multiarray technology for transforming complicatedgenomic data into valuable insights.

Paid and open-source bioinformatics toolsfurther support the sequencing data analysis for aligning and assembling DNAfragments. You can do variant calling, data visualizations, RNA expressionprofiling, gene fusion detections and data mining.

Bioinformatics tools help in thefollowing fields for performing genomic tests:

Molecular biology- Bioinformaticssoftware offers gRNA design tools for studying:

  • Restrictionenzyme map analysis
  • Codeon frequencytables
  • Sequencing primerdesign
  • Sequencescrambler

Peptide- Bioinformaticstool offer peptide library design tools for:

  • Amino acid code
  • Peptide propertycalculator
  • Antigenprediction

Common tools- Common tools inbioinformatics platform for Linux help with:

  • Nucleic acidconversions
  • Antibody drugdiscovery

Protein analysis- The applicationhelps with protein and RNA analysis for:

  • Psort II
  • WOLF-PSORT

Bioinformatics Tools and Applications

Bioinformatics tools with their genomic testing abilitieshave been helpful in finding genetic alternations that have strong link toserious disorders and diseases. Test genomic tools has various applications:

  • Sequence analysis- Sequence analysis is the method of subjecting an RNA, peptide sequence and DNA to different kinds of analytical methods. This is done to identify the origin, evolution and structure of biological databases.
  • Molecular modelling– Molecular modelling makes use of computational and theoretical methodologies for analyzing the behaviour of molecules. Best open source and free bioinformatics tools use the simulation technique for performing molecular modelling.
  • Molecular dynamics– Molecular dynamics application in bioinformatics determine the physical motion of atoms. The method is important for cell like environment in the field of structural bioinformatics. Measurements used here include graph theories, dynamic ross relations and perturbation response scans.
  • FASTA in bioinformatics– FASTA is a format that is text-based in nature and is used to represent peptide and nucleotide sequences. FASTA software packages for bioinformatics tools help here with sequencing protein and DNA alignments.
  • Phylogenetic analysis in bioinformatics– Phylogenetic analysis by bioinformatics tools provides branch diagrams for representing the relationship or evolutionary history between different organisms/species. These branch diagrams are called phylogenetic trees and they help identify characteristics like genes, organs, and proteins in an organization. 
  • Biological databases in Bioinformatics– Biological databases in bioinformatics can be best understood by analysing its three classifications that exist. The three classifications are- functional, structure and sequence. Protein sequences and nucleic acid is stored in sequence database whereas proteins & RNA exists in structural databases. Physiological role for gene products is provided by functional databases.

15 Free Bioinformatics Tools List 2022

Popular applications for bioinformatics are best for sequenceanalysis and curations. The best solutions in the field have key inbuiltcomputational and big data analysis tools for genome sequencing. Let us have alook at what else these applications are comprised of in the following list.

  • geWorkbench

Best for: Hierarchical clustering

Genome sequencing | GeWorkbenchGenome sequencing | GeWorkbench

geWorkbench bioinformatics software offers computational and java-based tools for visualizing, supporting and analyzing sequence data. The bioinformatics tool also supports various plug-ins for genomics and gene integration.

The open-source and free bioinformatics tool can also be used for basic statistical analysis and transcription factor analysis.

Features ofgeWorkbench:

  • Annotation pathways for collecting data
  • Self-organizing maps & T-tests
  • Hierarchical clustering
  • Gene ontology enrichment analysis
  • Microarray gene expression
  • Network reverse engineering

geWorkbench Download: geWorkbench download available for Linux, Mac OS X and Windows.

  • BioPerl

Best for: Computational molecular biology

Test genomic | BioPerlTest genomic | BioPerl

BioPerlbioinformatics tool for Linux is most deployed for computational molecularbiology. The standardized CPAN style is the unique selling point of thisbioinformatics platform. The Linux bioinformatics software offers Perl modulesfor peptide and nucleotide sequence data.

BioPerl Modules:

  • Parsing real BLAST output
  • Graphical rendering
  • EST clusters
  • Cytogenetic and radiation hybrid maps

BioPerl Download: You can install BioPerl on Linux, Unix and mac OS devices.

BioPerl Tutorial: Access BioPerl tutorial pdf.

  • UGENE Open Source Bioinformatics Tool for Linux

Best for: Dot plot & Chromatogram visualizations

Next-generation sequencing | UGENENext-generation sequencing | UGENE

UGENE open source and free bioinformatics tool Linux offers a common UI for integrating the platform with other bioinformatics applications. The software supports multiple formats for biological data available and you can retrieve it from remote locations. UGENE software sequence tool uses multicore GPUs and CPUs for the best performance.

Features of UGENEOpen Source Bioinformatics Tool:

  • Chromatogram visualization
  • Multiple align editor
  • Visual and interactive genomes
  • 3D viewing in MMDB and PDB formats
  • Phylogenetic tree view
  • Dot plot visualization
  • Query designer 

UGENE Download: UGENE software free download available for Linux, macOS and Windowsplatforms.

Unipro UGENE Tutorial: Access Unipro UGENE tutorial here.

  • Biojava Bioinformatics Tool for Linux

Best for: Ensemble databases

Bioinformatics databases | BiojavaBioinformatics databases | Biojava

Biojava Bioinformatics tool for Linux, Windows and Solaris is best known for its various java tools ideal for processing biological data. The genome sequencing software supports a range of datasets and parsers for the common file format. Biojava test genomic tool can also be used for managing statistical and analytical routines.

Biojava Modules:

  • Class objects and files for implementing java code
  • Server support and DAS clients
  • Ensembl databases
  • Sequence alignments
  • Homologene data

Updated Biojava Modules:

  • Multiple structural alignments
  • Support for protein assemblies
  • Updated structure data model
  • New structure file formats
  • Accessible surface area

Biojava Download: Biojava downalod is available for Solaris, Windows and Linux.

Biojava Examples: Some good examples of Java library in Biojava are:

  • Private static atom
  • Public residue identifier
  • Representative atom arrays
  • String sequence

Biojava Tutorial: Go to GitHub’s link shared here for accessing Biojava tutorial.

  • Biopython Test Genomic Software

Best for: Performing sequence analysis in bioinformatics

genome sequencing toolgenome sequencing tool

Biopython genome sequencing tool is most deployed for doing biological computation. This bioinformatics tool for Linux/UNIX supports multiple formats for bioinformatics files like FASTA, BLAST, Clustalw and Genbank. Inbuilt into Biopython are various python modules for making interactive and integrated sequences.

Features ofBiopython Test Genomic Software:

  • Managing sequence formats
  • Protein structure
  • Substitution matrices
  • Weight calculations, transcriptions and translations
  • EMBOSS command line tools

Biopython Uses:

  • Microarray data for clustering
  • Reading & writing tree-view files
  • Structure data for PDB analysis and parsing
  • BioSQL database
  • Parser development & sequence plus options

Biopython GitHub: Biopython uses git as it its source code

Biopython Documentation: Clear documentation based oncookbook-style

Biopython Download: Download Biopython package for Unix/Linux platforms.

  • InterMine

Best for: Integrating biological data sources

InterMine bioinformatics toolsInterMine bioinformatics tools

InterMinebioinformatics tools is used for analyzing and integrating biological data. Theopen source and free bioinformatics platform supports dynamic tables for datafiltering and drilling it down. The software functions by working with either asingle object or multiple lists in multiple languages.

Features ofInterMine:

  • Search tools for templates, keywords and queries
  • Support for GFF3, FASTA, Chado and such gene association files
  • General python codes

InterMine GitHub: Create an account on GitHub accessing InterMine Python for pythondevelopment.

InterMine Software Download: Youc can download InterMine by creating an account on GitHub.

InterMine Training Portal: InterMine training portalavailable for data query and analysis purposes.

  • IGV Genomic Sequencing Tool

Best for: Interactive genomics viewing

genomic sequencing applicationgenomic sequencing application

IGV genomicsequencing application offers genomics viewing for interactive genomics andeffective visualization. IGV has been built on next-generation sequencingtechnology for genomic annotation. IGV bioinformatics software also lets younavigate through extensive data set and zoom it as per your requirement.

Features of IGVTest Genomic Tool:

  • Attribute panel for tracking attributes
  • Sorting and grouping tracked data
  • File loading from genome space
  • Flexible integration of genomic data/metadata
  • Aligned sequence reads
  • Data set loading from remote/local sources
  • Multi-resolution file formats

IGV User Guide– Access IGV test genomic PDF.

  • GROMACS

Best for: Parameter files and topologies

bioinformatics tool for Linuxbioinformatics tool for Linux

GROMACSbioinformatics tool for Linux offers building and analysis tools for dynamicmolecular simulation. The bioinformatics software is used for moleculardynamics by simulating Newton’s motion from several particles. GROMACS performswell with lipids, proteins and such biochemical molecules for complexinteractions.

Features ofGROMACS:

  • Parameter files and topologies
  • File input & output through command line tools
  • Trajectory and routine analysis
  • MPI communication protocol
  • State of the art algorithms

GROMACS Download: GROMACS download is available for Windows, macOS and Linux.  

GROMACS Tutorial PDF: Access for GROMACS manual PDF.

  • Taverna Workbench

Best for: Silico experimentation

open source bioinformatics tool Linuxopen source bioinformatics tool Linux

Taverna Workbenchopen source bioinformatics tool Linux is deployed for streamliningbioinformatics workflows. The best part about using Taverna Workbench is thatit can be integrated with services like REST, WSDL and SOAP.

Taverna Workbench Features:

  • Silico experimentation
  • Command line executions
  • Java libraries
  • Semantically annotated components
  • X.509 client authentication
  • Debugging with workflow validation

Taverna Workbench Tutorial: Quick start guide for Taverna Workbench.

  • EMBOSS Bioinformatics Tool for Linux

Best for: Simplifying arrays and sequences

EMBOSS (European Molecular Biology Open SoftwareSuite) bioinformatics platform is ideal for the field of molecular biology andsciences. EMBOSS is most used for web page data sequencing. You can also usethis bioinformatics tools for nucleotide sequence pattern analysis.

Features of EMBOSS Open Source Bioinformatics Tool for Linux:

  • Domain analysis
  • Sequence alignment
  • Protein motif identification
  • Multiple structural and alignment formats
  • Programming libraries for database indexing
  • Simplified arrays and sequences

EMBOSS Software Download: Get EMBOSS software free download.

EMBOSS Bioinformatics Tutorial: Get EMBOSS manual here.

  • Clustal Omega

Best for: Multiple sequence alignments

genome testing software for Linuxgenome testing software for Linux

Clustal Omega in bioinformatics is a next generation sequencing tool designed for doing multi sequence alignments. The genome testing software for Linux supports different input sequence types such as HMM profile and aligning the sequence.

Features of Clustal Omega Alignment Tool:

  • Pairwise sequence alignment tools
  • Progress alignment for Clustal Omega result interpretation
  • Fast guide tree
  • HMM profile techniques
  • Clustal Omega phylogenetic tree generation

Get Clustal Omega: Available Clustal Omega Download.

  • BLAST

Best for: Finding match between protein & nucleotide sequences

BLAST or Basic Local Alignment Search Tool helps find similarity amongst biological sequences. The genome testing tool for Linux supports finding match between protein and nucleotide sequences. BLAST in bioinformatics tool also helps with structuring query sequences and mapping such data sets.

Features of BLAST Bioinformatics Tool:

  • Managing distance sequences
  • Protein-protein comparison and relation
  • Sequence aligning using protein constraint
  • Searching T cell receptors and immunoglobins
  • Finding conserved domains in a sequence

BLAST Bioinformatics Uses:

  • Searching protein sequence databases
  • Aligning query sequence
  • Detecting local aligment sequences

Blast Bioinformatics Tutorial: Get access to BLAST bioinformatics pdf.

  • Bedtool

Best for: Bedtools genomecov for computing historgrams

Bedtool bioinformatics platformBedtool bioinformatics platform

Bedtool bioinformatics platform is used for genomic testing and analysis purposes. The application supports different genome formats like VCF, GTF/GFF, BAM and BED. The bioinformatics software for Linux/UNIX and Windows can also be sued for shuffling genomic intervals of different files.

Features of Bedtool bioinformatics Software:

  • Targeted DNA capturing
  • GC content calculation
  • ChromHMM tracks
  • RNA-seq coverage analysis.
  • DNase hypersensitivity similarity calculation
  • Bedtools multicov for reporting alignment counts

Bedtools Download: Bedtools download is available for Windows, Unix and Linux.

  • Bioclipse Open Source Bioinformatics Tool

Best for: Biological sequencing

Bioclipse bioinformatics software for LinuxBioclipse bioinformatics software for Linux

Bioclipse bioinformatics software for Linux is a java-basedtool supporting biological sequences like protein, DNA and RNA. The genomesequencing tool is based on plugin architecture for semantic web functioning. Bioclipseis best used for representing molecular structures.

Features of Bioclipse Open Source Bioinformatics Tool

  • Single bench for accessing chemo toolkit
  • 3D visualization and 2D editing
  • Eclipse Rich Client platform

Bioclipse Download: Bioclipse download available for windows and macOS.

  • Bioconductor

Best for: Real-time biological metadata

Bioconductor is an open source bioinformatics tool that makesuse of R programming for analyzing data like oligonucleotide arrays and flowcytometer.  You can also deploy these solutionsfor generating powerful statistical and graphical database.

Bioconductor Bioinformatics Tool Features:

  • Digital gene expression
  • Real-time biological metadata
  • Comprehending high throughput genomic data
  • Genomic annotation
  • Reproducible research

Bioinformatics Bioconductor Package: Ape package aids, Adegenet, Affy and DEGseq.

Bioconductor Tutorial: Access Bioconductor tutorial.

Conclusion

Sequencing helps understand mutations and variations in human genes to identify disorders and serious diseases like cancers. Bioinformatics databases with their advanced sequencing techniques for genomic testing have proven critical for screening deadly diseases.

FAQs

  1. What is Genomic Testing?

    Genomic Testing is a type of test done to study mutations or alterations in genes to identify diseases, food-borne bacteria, and infections.

  2. What is the purpose of bioinformatics tools?

    For organizing vast molecular biological data, Developing tools required for analyzing the data and Accurate interpretation of results.

  3. How is bioinformatic tools used in genomics?

    Bioinformatics tools help perform genomic tests or next-generation sequencing for studying mutations in genes. These genes help predict the nature of a disease.

You can also check relevant categories:

Written by Jane