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The 20 Best Bioinformatics Tools for Linux System

There are far ranges of Linux bioinformatics tools available widely used in this field for a long while. Bioinformatics has been characterized in many ways; however, it is frequently defined as a combination of mathematics, computation, and statistics to analyze biological information. The main goal of the bioinformatics tool is to develop an efficient algorithm so that sequence similarities can be measured accordingly.

Best Bioinformatics Tools for Linux

This article has been written by focusing on the bioinformatics tools that are available on the Linux platform. All the efficient tools have been discussed and reviewed in detail. Moreover, you will find the essential features, properties and download links from this article. Hence, let’s go through it.

1. geWorkbench

geWorkbench can be elaborated with genome workbench is a java based bioinformatics tool that works for integrated genomics. Its components architectures facilitate specifically developed plug-ins that would be configured into complicated bioinformatics applications. Currently, seventy-plus plugs–ins are available for supporting, visualization, and analyzing sequence data.

geworkbench bioinformatics tool

Features of geWorkbench

  • It is included with many computational analysis tools, namely, t-test, self-organizing maps, and hierarchical clustering, and so on.
  • It is featured with molecular interaction networks, protein structure, and protein data.
  • It offers gene integration and annotation pathways and collects data from curated sources for gene ontology enrichment analysis.
  • In this tool, components get integrated with the platform management of inputs and outputs.

Get geWorkbench

2. BioPerl

BioPerl is a collection of Perl tools widely used in the Linux platform as a bioinformatics tool for computational molecular biology. It is continuously used in the bioinformatics fields into a set of standard CPAN-style. This Linux bioinformatics tool is well documented and freely available in Perl modules. Because of being object-oriented, these modules are interdependent to accomplish the task.

bioperl bioinformatics tool

Features of BioPerl

  • From the local and isolated databases, this bioinformatics tool access nucleotide and peptide sequence data.
  • It manipulates distinct sequences along with transforming the form of database and file record too.
  • It works as a bioinformatics search engine where it looks for similar sequences, genes, and other structures on genomic DNA.
  • By generating and manipulating sequence alignments, it develops machine-readable sequence annotations.

Get BioPerl


UGENE is a free open source and a set of integrating bioinformatics tools for Linux. Its common user interface is integrated with mostly used and well- familiar bioinformatics applications. Numerous biological data formats are compatible with its toolkits; thus, data can be retrieved from remote sources. This bioinformatics tool utilizes multicore CPUs and GPUs to provide maximum possible performance to optimize its computational activities.

ugene bioinformatics tool

Features of UGENE

  • Its graphical interface user offers several features, for instance, chromatogram visualization, multiple align editor, and visual and interactive genomes.
  • It paves the way for a 3D view in PDB and MMDB formats along with anaglyph stereo mode support.
  • It facilitates Phylogenetic tree view, Dot plot visualization, and query designer can search for intricate annotation patterns.
  • It can pave the way for custom computational workflow for the workflow designer.


4. Biojava

Biojava is an open source and exclusively designed for the project to provide the required java tools to process biological data. It works for far ranges of datasets, for instance, analytical and statistical routines, parsers for common file formats. Moreover, it facilitates the manipulation of sequence and 3D structure. This bioinformatics tool for Linux aims to expedite swift application development for biological datasets.


Features of Biojava

  • Including class files and objects, it is a package that implements java code for a variety of datasets.
  • Biojava can be used in different projects such as Dazzel, Bioclips, Bioweka, and Genious that are used for various purposes.
  • It works for file parsers along with the DAS clients and server support.
  • It is used for making sequence analysis for GUIs and can access BioSQL and Ensembl databases.

Get Biojava

5. Biopython

Biophython bioinformatics tool developed by an international team of developers and written in python program is used for biological computation. It offers access in a fair range of bioinformatics file formats, namely, BLAST, Clustalw, FASTA, Genbank, and allows access to online services such as NCBI and Expasy.

biopython bioinformatics tool

Features of Biopython

  • It is accumulated with python modules that work on making a sequence with interactive and integrated nature.
  • This bioinformatics tool can perform in different sequences, for instance, translation, transcription, and weight calculations.
  • This tool is exclusively enriched; thus, protein structure and sequence format get managed efficiently.
  • This Linux bioinformatics tool works for alignments; thus, a standard can be established to create and deal with substitution matrices.

Get Biophython

6. InterMine

InterMine is an open-source bioinformatics tool for Linux that works as a data warehouse to integrate and analyze biological data. Being software, users can install it on their device and make data available on the web page. It is believed one of the most dynamic data tables that can easily drill down into data, and it smoothes the way of filtering data. What is a more additional column to navigate towards the report page?


Features of InterMine

  • It works with a single object, for instance, a gene, protein, or binding site, and multiple lists such as a list of genes or a list protein.
  • It can be operated in multi-languages; thus, different queries regarding biometrics information can be searched in a couple of languages.
  • In this software, four search tools are available: template search, keywords search, query builder, and region search.
  • It supports different formats such as Chado, GFF3, FASTA, GO & gene association files, UniProt XML, PSI XML, In Paranoid orthologs, and Ensembl.

Get Intermine

7. IGV

IGV, elaborated as an interactive genomics viewer, is believed one of the most effective visualization tools that can easily access an extensive and interactive genomics database. It can offer a wide variety of data types with genomic annotation along with array-based and next-generation sequence data. Just like Google Maps, it can navigate through a data set and smooth the way of zooming and panning seamlessly across the genome.

igv bioinformatics tool

Features of IGV

  • It offers flexible integration of far ranges of genomic datasets, including aligned sequence reads, mutations, copy numbers, and so on.
  • It expedites to enable real-time exploration regarding the massive supportive dataset by using efficient and multi-resolution file formats.
  • Among hundreds and, to some extent, up to thousands of samples, it lets simultaneous visualization of various data types.
  • It allows loading datasets from local and remote sources, including cloud data sources, to observe own and publicly available genomic datasets.



GROMACS is a dynamic molecular simulator that is included with analysis and building tools. It is a package with versatility and intends to work on molecular dynamics; for instance, it can simulate the Newtonian equation of motion from hundreds to thousands of particles. It was programmed to perform on biochemical molecules at the earlier stage, namely protein and lipids, bonded with complicated interactions.

gromacs bioinformatics tool

Features of GROMACS

  • This Linux informatics tool is user-friendly, containing topologies and parameter files, and it is written in cleartext.
  • Script language has not been used; thus, all programs are operated with a simple interface command-line option for input and output files.
  • If anything goes wrong, then many error messages and consistency checking get done.
  • All programs are facilitated with the integrated graphical user interface.


9. Taverna Workbench

The Taverna Workbench is an open-source tool that is programmed to design and execute bioinformatics workflows created by the myGrid project. A range of software can be integrated with this tool, including SOAP and REST web service. It collaborates with distinct organizations such as the European Bioinformatics Institute, the DNA Databank of Japan, the National Center for Biotechnology Information, SoapLab, BioMOBY, and EMBOSS.

taverna bioinformatics tool

Features of Taverna Workbench

  • It is entirely designed with the graphical workflow to finding, developing, and executing workflows.
  • It has been designed with an entirely graphical workflow; moreover, discrete tabs are used for design.
  • Annotations are given for describing workflows, services, inputs, and outputs with a built-in help facility.
  • Previously used workflow is stored in this tool, even if it can save inputs workflow used in the file.

Get Taverna Workbench


EMBOSS that implies European Molecular Biology Open Software Suite. It is a package of software that has been developed for the molecular biology community’s needs. This Linux bioinformatics tool can be used for different purposes. For instance, it is functional in various formats of data automatically. Moreover, it can collect data sequentially from the web page.

Features of EMBOSS

  • EMBOSS is included with hundreds of applications, namely, sequence alignment and rapid database searching with sequence patterns.
  • Additionally, it has protein motif identification, including domain analysis and nucleotide sequence pattern analysis.
  • Its toolkit has been designed appropriately to address the bioinformatics application and workflow.
  • It has been programmed with additional libraries to handle many other relevant issues as well.


11. Clustal Omega

Clustal Omega works on protein, and RNA/DNA is a multiple sequence alignment program designed for general purposes. It efficiently can handle millions of datasets in a reasonable time; moreover, it produces high-quality MSAs.  In this Linux bioinformatics tool, there is a process where the user requires leaving the file sequence in the default mode. That gets aligned and clustered to generate a guide tree, and that ultimately allows forming a progressive alignment sequence.

Features of Clustal Omega

  • It facilitates aligning existing alignments with each other and, what is more, aligning a sequence to an alignment for using a hidden Markov Model.
  • There is a feature that is called external profile alignment that refers to a new sequence of homologous for the hidden Markov Model.
  • HMMs are used for the Clustal Omega for the alignment engine taken from the HHalign package from Johannes Soeding.
  • Clustal Omega allows three types of sequence inputs: the profile, align the sequence, and HMM.

Clustal Omega


Basic Local Alignment Search Tool or BLAST is used for finding the similarity among biological sequences. It can find relevant matches between nucleotide and protein sequences and show the statistical importance of it. Query sequences are structured with different types of BLAST. What is more, this tool is largely cultivated thriving unknown genes in various animals, and it lets mapping out sequence-based datasets through qualitative analysis.

blast bioinformatics tool

Features of BLAST

  • The megaBLAST nucleotide-nucleotide offers to search and optimizing for very similar types of sequences.
  • Additionally, the BLASTN nucleotide-nucleotide works a little different way as it looks for distance sequences.
  • What is more, BLASTP performs finding protein-protein relation and comparison, and its formula is used for different other research.
  • TBLASTN focuses on the nucleotide query against the protein dataset, and it can translate the database on the fly.


13. Bedtools

Bedtool bioinformatics software is a Swiss army knife of tools used for far ranges of genomic analysis. Genomic arithmetic uses this tool very widely that implies it can find the set theory with it. For instance, bedtools facilitate one to count, complement, and shuffle intersect, merge genomic intervals from multiple files, and generate a particular genome format such as BAM, BED, GFF/GTF, VCF.


Features of Bedtools

  • In this Linux bioinformatics tool, each is designed to perform a particularly simple task, e.g., intersect two interval files.
  • The complicated and sophisticated analysis gets done by using a combination of bedtools.
  • This tool is developed in Utah University’s Quinlan laboratory by a group researcher.
  • Since there are many options in this tool, it can be used for multi-purposes in the bioinformatics field.

Get Bedtools

14. Bioclipse

Bioclipse Linux bioinformatics tool that is defined with workbench for life science is a java based open-source software. It works on the visual platform that includes chemo and bioinformatics Eclipse Rich Client Platform. It is featured with a plugin architecture. That implies the state of the art plugin architecture moreover, functionality and visual interfaces from Eclipse, such as help system, software updates also included.


Features of Bioclipse

  • Biological sequences, namely, RNA, DNA, and protein, are managed with the bioclipse.
  • Biojava assists in providing core bioinformatics functionality also; graphical editors for sequence alignments as well.
  • It is used for pharmacology and drug discovery along with the site of metabolism discovery.
  • Finally, it works on semantic web functionality, browsing extensive compound collections, and editing chemical structures.

Get Bioclipse

15. Bioconductor

Bioinformatics used extensively in the Linux platform is an open-source and free bioinformatics tool, coherently used in medical biology for high-throughput analysis.  It mainly uses statistic R programming; nevertheless, it also contains another programming language as well.  This software is designed by focusing on a couple of objectives; for instance, it aims to establish a collaborative development and to ensure of using innovative software immensely.


Features of Bioconductor

  • This software can analyze a range of data, for instance, oligonucleotide arrays, Sequence analysis, flow cytometer and can generate a robust graphical and statistical database.
  • Having vignettes and documents in each and Binocular package can provide textually and task-oriented description of that package functionality.
  •  It can generate real-time data regarding the associating microarray and other genomic data along with biological metadata.
  • Additionally, it can analyze express genes such as LIMMA, cDNA Arrays, Affy Arrays, RankProd, SAM, R/maanova, Digital Gene Expression, and so on.

Get Bioconductor


AMPHORA that stands for Automated Phylogenomic infeRence Application is an open-source bioinformatics workflow tool. Another version of AMPHORA that is called AMPHORA2 has bacterial and 104 archaeal phylogenetic marker genes. More importantly, it works to create information between phylogenetic and met genetic datasets.

Features of AMPHORA

  • Because of being single genes, AMPHORA2 is the most suitable for deducing the taxonomic composition of bacteria.
  • Moreover, it also can infer the taxonomic composition of archaeal communities from the metagenomic shotgun sequence.
  • Initially, AMPHORA was used to analyze the Sargasso Sea metagenomic data.
  • However, nowadays, AMPHORA2 is increasingly used to analyze relevant metagenomic data in this regard.


17. Anduril

Anduril is open source components-based bioinformatics software for Linux that works for creating a workflow framework regarding scientific data analysis. This tool is developed by the Systems Biology Laboratory, University of Helsinki. This bioinformatics tool for Linux is designed to enable efficient, flexible, and systematic data analysis, particularly in the biomedical research field.

anduril bioinformatics tool

Features of Abduril

  • It works in a workflow where different processing system is interrelated; for instance; an output of a process can work as an input of others.
  • The primary Anduril tool is written in Java, whereas other components are written in different applications.
  • In its various steps, numerous activities take place, such as; it creates data, generate reports, and import data too.
  • Its workflow configuration can be done with a simple overtness, powerful scripting language, namely, Andurilscript.

Get Anduril

18. LabKey Server

LabKey Server is a preferred choice for the scientists used in the laboratories to integrate research, analyze and share biomedical data.  A secure data repository is used in this tool that facilitates web-based querying, reporting, and collaborating within a far range of databases. Along with the given underlying platform, many more scientific instruments can be added in this application.


Features of LabKey Server

  • LabKey Server is featured with all types of biomedical data. For instance, flow cytometry, microarray, mass spectrometry, microplate, ELISpot, ELISA, and so on.
  • In this tool, a customizable data processing pipeline executes all the relevant activities.
  • It is featured with observational studies that support the management of longitudinal, large-scale studies of participants.
  • Proteomics is used for processing high-throughput mass spectrometry data using a specific tool, namely, X! Tandem.

Get LabKey Server

19. Mothur

Mothur is an open-source bioinformatics tool widely used in the biomedical field for processing biological data. It is a software package that is frequently used for analyzing DNA from uncultured microbes. Mothur is a Linux bioinformatics tool that can process data generated from DNA sequence methods, including 454 pyro-sequencing.

mothur bioinformatics tool

Features of Mothur

  • It is a single package software capable of handling community data analyzing and making a sequence.
  • Large-scale community documentation support and another form of support are provided with this tool.
  • It is believed Mothur is the most prominent bioinformatics tool analyzing 16S rRNA gene sequences.
  • A dedicated community and tutorials are available in this tool to inform how to use Sanger, PacBio, IonTorrent, 454, and Illumina (MiSeq/HiSeq).

Get Mothur


VOTCA stands for Versatile Object-oriented Toolkit for Coarse-graining Applications, which is branded as an efficient bioinformatics tool with a Coarse-grained modeling package that mainly analyzes molecular biological data. It aims to develop systematic coarse-graining techniques along with simulating microscopic charge to transport disordered semiconductors.

Features of VOTCA

  • VOTCA is mainly featured with three major parts: the Coarse-graining toolkit, the Charge Transport toolkit, and the Excitation Transport Toolkit.
  • All three core features are from the VOTCA tool library that implements shared procedures.
  • VOTCA uses coarse-graining methods to harvest the best outcomes from relevant activities.
  • This software is featured with an excitation transport toolkit where orca DFT packages get supported by it to a significant extent.


Final Thought

To encapsulate the whole thing, it is worth mentioning here that all the forth mentioned bioinformatics applications are extensively used in this field. These Linux bioinformatics tools are used in medical science, pharmacology, drug invention, and relevant sphere for a long while. Finally, you are requested to leave your two pennies regarding this article. What is more, if you find this article is worthwhile, please do not forget to like, share, and comment on it. Your precious comment will be appreciated.


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