Are you looking forward to making some phenomenal contributions to the field of medical sciences using computational skills? Then you are at the right spot at the right time. Today we shall discuss the best bioinformatics software and tools available for biological data analysis and research.
Honestly, there are hundreds of tools and software available to perform complex biological research operations. However, choosing the most optimum and accurate tool can be tricky for you if you are new to the research world.
We shall make this task easier for you today. Here is a list of the 30+ best bioinformatics software and tools that are popular as well as highly efficient. So let’s get straight into digging about them more!
What are The Best Bioinformatics Software and Tools?
Hundreds of tools are available for computational analysis. However, only a few are recognized and regularly used by reputed scientific communities around the world. The highly cited tools with reliable results in research papers are the best bioinformatics software.
Computer programmers and software developers are perpetually striving to improve their accuracy. Given below is a list of the best bioinformatics tools that are globally recognized and used for analysis.
1. GALAXY
GALAXY is a popular bioinformatics tool extensively used for data integration and analysis persistence for computational biology research. It is compatible with UNIX-like operating systems. It is available on the web browser too.
It is a workflow system for bioinformatics that provides a graphical user interface for specifying each step. The platform supports a variety of biological data formats, translation, and data integration.
The applications of Galaxy are in the study fields of- Gene expression, proteomics, transcriptomics, next-generation sequencing analysis, genome assembly and more.
- It is an open source free to use
KEY FEATURES
- Easy-to-use graphical interface
- Performs accessibility, reproducibility, and transparency in research
- All analysis steps and parameters are specified
- Extensible software with new tools integration possibilities
What Is Unique About GALAXY?
An extensive bioinformatics workflow management system for heavy computational analysis using data integration and interoperability.
Who GALAXY Is Best For?
Chemoinformaticians, drug designers and computational chemists can use it since applied overboard to the field of Cheminformatics.
2. Ascalaph Designer
Ascalaph Designer is a bioinformatical/computational program for molecular modelling and simulation. The platform runs on single and multiple processors. Compatible with Windows platform.
It performs various molecular modelling tasks such as design, modelling, quantum calculations and force field development. A platform that provides a graphical environment for quantum and classical modelling ORCA, Firefly, CP2K, etc.
A step-by-step tutorial is provided for beginners to learn molecular modelling from scratch. It can be used for studies in lipid bilayers, ionic liquids, polyelectrolytes, proteins and nucleic acids.
- It is an open source free to use
KEY FEATURES
- General-purpose, highly scalable without getting affected by parameters
- Geometrically optimised for best results
- Molecular dynamics modelling with multiple steps
- Quantum modelling- new and unique feature
- Molecular graphics and model building
What Is Unique About Ascalaph Designer?
Parallel molecular dynamics on Linux clusters with MDynamix. Scaling is good, size of the system and number of processors do not affect it.
Who Ascalaph Designer Is Best For?
Recommended for the study of molecular modelling (specifically proteins) and simulations of structures by structural biologists.
3. AutoDock
AutoDock is one of the most cited software by the research community. A computational molecular modelling simulation software that is compatible with all operating systems. The latest version AutoDock4 is available for use.
The modified version, AutoDock Vina is popularly used. The software has two main components. The first part is for docking the ligand to a set of grids of the target protein. The second part is for pre-calculating the grids.
The software works on sophisticated gradient optimisation methods and calculation of the gradient effectively gives a sense of direction.
- It is an open source free to use
KEY FEATURES
- Facilitates both molecular docking and virtual screening
- Improvement in calculations using openCL and CUDA
- Improved local search on AutoDock Vina
- Runs faster under 64-bit operating systems in Linux
- Open for improvement in software by third-party
What Is Unique About AutoDock?
AutoDock Vina adapts itself according to the input file. There are no limitations of manually editing the source PDBQT file.
Who AutoDock Is Best For?
Best recommended for drug discovery and design by pharmacists since it has been used for the discovery of drugs including HIV1 integrase inhibitors.
4. BioJava
BioJava is a bioinformatical platform dedicated to processing diverse biological data using Java tools. Written in Java language, it is compatible with the web browser platform with a Java run environment.
Various operations such as sequence manipulation, protein structure analysis, Distributed Annotation System (DAS), dynamic programming, and Common Object Request Broker Architecture (CORBA) interoperability are performed.
Projects accomplished using BioJava platform- Strap, Geneious, GenBeans, Cytoscape, Bioclipse and more. Modify BioJava from the GitHub repository to add better analysis components.
- It is an open source free to use
KEY FEATURES
- Enables protein structure parsing and manipulation
- Similar sequences search and manipulation of individual sequences
- Creating and editing multiple sequence alignments
- Data retrieval from databases for nucleotide and protein sequences
- Easy conversion of file formats
What Is Unique About BioJava?
The multiple functionality makes it easy to create customised pipelines for the analysis of genomic data.
Who BioJava Is Best For?
Many renowned bioinformatics projects have been accomplished using BioJava. An ideal tool for core computational biologists.
5. AMPHORA
AMPHORA AutoMated Phylogenomic infeRence Application workflow is suitable for Linux environment. The core of the tool is a protein phylogenetic marker database that constitutes curated protein alignments with trimming mask and profile HMM models.
It utilises bacterial phylogenetic marker genes for deriving phylogenetic information from metagenomic data sets. Efficient in building concatenated phylogenetic genome trees using multiple protein markers.
Since marker genes are single copies, the accurate bacterial taxonomic composition of metagenomic shotgun sequencing data can be inferred by employing AMPHORA2.
AmphoraVizu is a web server platform that allows to visualisation of the outputs generated by the AMPHORA2 or the webserver mode Amphora Net.
- It is an open source free to use
KEY FEATURES
- Automated pipeline for phylogenomic analysis
- Overcomes the bottlenecks limiting large-scale protein phylogenetic analysis
- High throughput and high-quality results
- Rapid and accurate generation of highly reproducible MSA for phylogenetic markers
- AMPHORA2 is a free software available for modification and redistribution
What Is Unique About AMPHORA?
If you are not well aware of the Linux environment, no problem! AmphoraNet is the web server implementation of AMPHORA2. Easy to use on a web browser with default options just like AMPHORA2.
Who AMPHORA Is Best For?
Recommended for metagenomic study to find out what organisms exist in the current environment and their roles. Evolutionary biologists can find it helpful.
6. EMBOSS
EMBOSS European Molecular Biology Open Software Suite is the complete bioinformatical analysis package developed for molecular biology and bioinformatics users. Tutorials, manuals and extensive support provided to the user community.
More than 200 applications for molecular analysis and basic bioinformatics operations are available. Sequence alignment, database searching, protein motif identification, domain analysis and much more are available.
It has C programming libraries with powerful APIs. Many inbuilt functionalities and convenient platform. Many interfaces are available, easy-to-use web interfaces and powerful workflow software.
- It is an open source free to use
KEY FEATURES
- Comprehensive set of sequence analysis programs
- Powerful database indexing software
- Graphical interface and easy-to-use web-based interfaces
- Allows local database systems for data retrieval
- High-quality and reliable results
What Is Unique About EMBOSS?
Many available packages and tools are integrated with EMBOSS enabling powerful workflow for constructing pipelines
Who EMBOSS Is Best For?
Includes different types of analysis packages hence any biological/computational researcher can use EMBOSS for specific types of analysis.
7. Integrated Genome Browser
Integrated Genome Browser is the visualisation tool for picturing amazing biological patterns in genomics datasets, sequence data, Gene models, and DNA microarray data. The software is compatible with UNIX, Linux, Mac, and Windows operating systems.
This tool is fast and reliable for visualising the vast data on a desktop. It loads local files as input from the internet. It supports dozens of file formats and also converts output data files for visualisation.
Motif and site searches, BLAST search, publication-based high-quality images and sharing of visual output files is possible among multiple users. Mostly used for observing interacting patterns between protein sequences and nucleotides.
- It is an open source free to use
KEY FEATURES
- The Java library is integrated and implements visualisation features
- Visualisation of high throughput sequencing data from Illumina and other platforms
- Supports input formats- BAM, BED, FASTA, GTF, GFF, SGR, WIG, file formats
- Output file format supported- EPS, PDF, SVG, PNG, GIF, BPM, SWF and more
What Is Unique About Integrated Genome Browser?
Dynamic, real-time zooming and scrolling genomic maps are some of the distinct visualisation formats that make it unique from similar tools.
Who Integrated Genome Browser Is Best For?
An effective tool for SNP, RNA Seq data visualisation, can be used by Next Generation Sequencing data experts.
8. Bioconductor
Bioconductor is a statistical R programming language-based bioinformatics tool. Compatible with Linux, Windows, and macOS platforms. It is used for the analysis of high-throughput biological data generated in molecular biology wet lab experiments.
Many versions of Bioconductor have been released. Each year, two versions of the software are launched. Genome annotation packages are available for different types of microarrays- cDNA/Oligo.
The functional scope of the software packages has widened including analysis of SAGE, sequence and SNP data. The platform trains researchers on computational methods and statistical applications for the analysis of huge genomic data.
- It is an open source free to use
KEY FEATURES
- Provides a powerful range of statistical and graphical methods for genomic data analysis
- Includes metadata from PubMed, annotation data from Entrez
- Provides rapid development and deployment of scalable and interoperable software
- High-quality documentation and reproducible research
What Is Unique About Bioconductor?
The use of packages provides a basic understanding of the command language in R programming. Without expertise and knowledge in programming, biologists can analyse data.
Who Bioconductor Is Best For?
Bioconductor packages having strong computing facilities can be used by data biologists to analyse different datasets.
9. GenePattern
GenePattern is a powerful scientific workflow system for access to genomic analysis tools. It can be used to design sophisticated pipelines for research experiments that include methods, parameters, data usage, and result generation.
GenePattern repository is created for discussion on module modifications. A public web application hosted by Amazon Web Services.
Over 200 visualisation tools for data processing and pre-processing. Automated history and tracking that enables users to share and understand the complete analysis process. No programming experience is required for web interface analysis.
- It is an open source free to use
KEY FEATURES
- Up-to-date repository of computational analysis modules
- Data preprocessing, gene expression analysis, SNP analysis, short read sequencing and flow cytometry
- Users can create accounts, perform analysis, create pipelines and save
- Multiple interfaces available as web browsers, applications, and programmatic interfaces
What Is Unique About GenePattern?
GenePattern notebook environment allows researchers to run the analysis within notebooks that interleave graphics, text and execute codes for a single research narrative.
Who GenePattern Is Best For?
Computational biologists and developers from Java, MATLAB, and R can use the analysis modules on programmatic interfaces
10. Geworkbench
Geworkbench is a biological software for integrated genomic data analysis compatible with Windows, Linux, and macOS platforms. Written in the programming language Java, this software is a desktop application that uses a component architecture.
There are more than 70 plug-ins included with the software that provide analysis and visualisation for gene expression data, sequence, and structure.
The National Centre for the Multiscale Analysis of Genomic and Cellular Networks manages this platform. Several biological tools for system and structural biology analysis are available within the plug-ins.
- It is an open source free to use
KEY FEATURES
- Provides molecular interaction networks, gene expression visualisation
- Protein sequence and protein structure data available
- Component integration through platform management
- Dataset history tracking with complete records
- Basic bioinformatics tools such as BLAST search are available
What Is Unique About Geworkbench?
Allows integration with third-party tools such as Cytoscape, genome space and gene pattern that helps in accurate result generation
Who Geworkbench Is Best For?
Effective tool for functional biologists since integration of pathway annotation information by Gene ontology enrichment is available
11. GROMACS
GROMACS is a versatile package to perform molecular dynamics and simulations. It is compatible with Linux, Windows, macOS and other UNIX varieties. It is one of the popular bioinformatics tools available for worldwide research.
The tool is designed for analysis of complicated bond interactions in proteins, lipids, nucleic acids and polymers. It is fast at calculating simulations in non-bonded interactions. It provides high performance due to algorithmic optimizations.
The up-to-date algorithms are integrated into the tool for extended simulation processes for enhancement in results with high accuracy.
- It is an open source free to use
KEY FEATURES
- Simple to use interface with the command line options
- The expected time for accomplishing a task is given
- The coordinates are stored in a compact way
- Accuracy can be manually selected by the user
- Fully automated topology builder for proteins
- Enhanced performance in simulations without sacrificing accuracy
What Is Unique About GROMACS?
It provides a large selection of flexible tools for trajectory analysis. No post-processing for output is required since the graphs are well-labelled.
Who GROMACS Is Best For?
Many publications have discussed the brilliant features of GROMACS. Every Bioinformatician can use this software for MD simulations.
12. Clustal
Clustal is a popular bioinformatics tool used widely for Bioinformatical processing for Multiple Sequence Alignments. It is compatible with several computing platforms of UNIX, Linux, MacOS, Windows and similar operating systems.
The entire package of Clustal has several tools integrated into it. ClustalV, ClustalW, and Clustal Omega are a few of them. Clustal 2/Clustal X is also known popularly for its remarkable features. The current standard version is Clustal Omega. Go for it if you are thinking to use it.
Clustal has been very highly cited in scientific publications. It builds UPGMA cluster analysis based on guided trees of pairwise sequence alignments. Updated algorithms of alignment are integrated with the software.
- It is an open source free to use
KEY FEATURES
- Sequence alignment by heuristic method to build MSA
- Utilizes distance matrix to build UPGMA and NJ-based trees
- Steps are carried out automatically on choosing appropriate options
- A wide range of input files accepted- FASTA, NBRF, PIR, EMBL, GDE, RSF, GCC, Clustal and more
- Output formats are also wide- NBRF, PIR, PHYLIP, GDE, NEXUS
What Is Unique About Clustal?
Optimal results are obtained with high accuracy due to optimized algorithms. Highly excellent results when data sets have varied degrees of divergence.
Who Clustal Is Best For?
Evolutionary biologists can take maximum benefit from this tool to construct guided trees and almost optimum graphical representations of evolutionary divergence.
13. FastQC
FastQC is a popular quality control tool for high-throughput sequence data obtained by next-generation sequencing techniques. The tool is written in Java language and requires a Java runtime environment. Available on both command-line and web browsers.
Compatible with Windows, Linux, and macOS platforms. The tool provides a simple method to control quality checks of raw data coming directly from sequencing pipelines. Manual guides are available for beginners to understand the pipeline.
Easy to download and user-friendly interface for tackling data before further analysis. The input files contain read sequences and the output is obtained in the form of graphics and tabular summaries of results.
- It is an open source free to use
KEY FEATURES
- Provides a quick overview of the file content
- Summary in tabular format and graphs for quick assessment
- Supports BAM, SAM or fastQ files of any type
- Results can be saved in HTML format and viewed at any time
What Is Unique About FastQC?
FastQC tool works in off-line mode and generates automated reports without running the application
Who FastQC Is Best For?
The foremost requirement before further analysis is the quality check of sequences hence biological data analysts can use the software for assessment.
14. SPAdes
SPAdes is a genome assembly toolkit that has various genome assembly pipelines. Platforms compatible with SPAdes are either Linux or macOS and Python. The platform reads IonTorrent and Illumina-generated files. Provides hybrid assemblies using Oxford Nanopore Technology and Sanger reads.
Supports files containing paired-end reads, unpaired reads, and mate pairs. Built for small genomes such as bacterial, fungal and others. Not meant for large genomes. SPAdes provides the pipeline with several modules for read error correction from Illumina reads and IonTorrent reads.
Easy to install and use by the command line. It supports various file formats and results can be obtained in convertible formats.
- It is an open source free to use
KEY FEATURES
- Various separate modules are available for read error correction
- Mismatch corrector module for improving mismatch
- High-quality assemblies can be obtained
- Download the source code and compile it yourself
- Supports various varied formats from different platforms
What Is Unique About SPAdes?
You can use read error correction stage only if you want to use another assembler for genome assembly. Great complexity is choosing the parameters.
Who SPAdes Is Best For?
Microbiologists and virologists can take advantage of this tool for assembling the genomes of microorganisms.
15. Velvet
Velvet is a de Novo genomic assembly bioinformatics tool designed for short-read sequencing technologies. Compatible with Linux and macOS platforms.
The input is short reads from which errors are removed and high-quality contigs are produced. Repeated areas between contigs are retrieved when paired-end reads are available. It is easy to download Velvet and view the source code.
Very little information is lost during assembly correction. Plot the k-mer coverages distribution to detect any errors in them.
- It is an open source free to use
KEY FEATURES
- Input sequence files are fasta (default), BAM, SAM, and fastq formats
- Paired-end reads are better for enhanced results ‘
- All coverage values are provided in k-mer coverage (no. of times k-mer seen in reads)
- Outputs in .afg file format that can be converted with open sources to different formats
- Bundled with programs beneficial to multiple user types
What Is Unique About Velvet?
Velvet is designed exclusively for cautiously removing errors from the assembly and losing little information during the process.
Who Velvet Is Best For?
Velvet can be used by computational biologists and bioinformaticians for assessing very short reads and obtaining contigs for further analysis.
16. MG-RAST
MG-RAST allows automatic analysis of metagenomes for phylogeny and functional studies. The tool performs rapid annotations using subsystem technology. It performs sequence comparisons using databases for both nucleotides and amino acids.
The application provides quality control, comparative analysis, annotation and safe storage of metagenomic and amplicon sequences with the help of their integrated bioinformatics tool. The web server is maintained by Argonne National Laboratory.
It effectively reduces bottlenecks in metagenome analysis such as the presence of high-performance computing for annotation data. It is also a repository for metagenomic data. It collects and interprets genomic data for studies, and maintains and curates the information.
- It is an open source free to use
KEY FEATURES
- Supports Metatranscriptomics and amplicon sequence
- Low-quality regions are trimmed and inappropriate lengths removed
- Identifies sequences in the gene using a machine-learning approach
- A specific program is used to identify gene annotation and functions
What Is Unique About MG-RAST?
The tool also performs data discovery, visualisation and comparison of metagenomic profiles hence, the automatic feature is remarkable of the tool.
Who MG-RAST Is Best For?
The tool is used for automatic annotation and metagenomic analysis so microbiologists, computational biologists and bioinformaticians can use it effectively.
17. MUSCLE
MUSCLE (Multiple Sequence Comparison by Log-Expectation) tools are one of the most popular and much-used tools in bioinformatics. It is meant with the purpose of Multiple Sequence Alignment of sequences of proteins and nucleotides.
Very high accuracy and high speed of alignment for thousands of sequences within seconds. Very few command-line features are used otherwise, only the manual choices can execute the alignment jobs.
The entire execution cycle is divided into three stages- draft progressive, improved progressive and refinement stage. Integrated with several other genes such as- Lasergene, MEGA, UGENE, Geneious, and more.
- It is an open source free to use
KEY FEATURES
- Different well-defined stages for executing the alignment task- three main stages
- Kimura distance is employed for re-estimating the binary tree
- Gives better results for Multiple Sequence Alignment as compared to other tools
- User-friendly and easy interface
- Available on web browsers not needed for separate installation
What Is Unique About MUSCLE?
MUSCLE is a fast tool for large sequences and aligns hundreds of multiple sequences at a single time within a few seconds. Shows high accuracy and precision in results.
Who MUSCLE Is Best For?
For performing any basic and fundamental analysis of sequence MUSCLE can be used by analysts and biological data experts such as Bioinformaticians.
18. Burrows Wheeler Aligner
Burrows Wheeler Aligner package is a tool for mapping low divergent sequences against large reference genomes from different organisms. This involves three major algorithms called BWA backtrack, BWA-SW, and BWA-MEM.
For longer Illumina sequence reads, the BWA backtrack algorithm is used. For longer sequences, other two algorithms are widely used. Each of the algorithms is great for usage however, BWA-MEM is recommended due to high accuracy and sequence read quality.
The obtained results are in the SAM file format that is supported by general SNP calling platforms such as SAM tools and GATK. BWA is used during NGS data analysis.
- It is an open source free to use
KEY FEATURES
- BWA-MEM and BWA-SW have similar characteristics such as split alignment
- BWA-MEM is recommended due to its high quality and accuracy
- Fast and accurate methods for alignment of long reads from different sequencers
- Long reads are smoothly aligned with a sequencing error rate below 2%
What Is Unique About Burrows Wheeler Aligner?
BWA algorithms work effectively with reference genome length over 4GB however, chromosome size must be 2GB at maximum.
Who Burrows Wheeler Aligner Is Best For?
BWA tool can be used for effective next-generation sequencing data analysis by Bioinformaticians and computational biologists.
19. Pilon
Pilon software tool is used for finding variations in different strains and large difference detections. It is also employed for improving draft assemblies by automatic methods.
It requires a fasta file as input of the genome along with an additional BAM file of read aligned to the input fasta file. It is easy to identify inconsistencies between the genome and the reads by read alignment analysis.
Improvement in the input genome is provided by the tool such as- small indels, large indels, single base difference, gap filling, local misassemblies, new gaps opening and more. The output format is a fasta file that contains an improved representation of the genome and VCF detailing variations between reads and input genome files.
- It is an open source free to use
KEY FEATURES
- Various input and output file formats are available
- Manual inspection and editing allow for better results
- Major improvements in the input genome can be made
- Changes can be viewed on IGV and GenomeView platforms
What Is Unique About Pilon?
For inspection and analysis, Pilon provides tracks that can be displayed on Genome viewers such as IGV.
Who Pilon Is Best For?
Biologists working on microbial and viral genomes can use the tool to identify variations between the reference genomes and query sequences.
20. BLAST
Basic Local Alignment Search Tool (BLAST) is a popularly used bioinformatical platform for searching similar sequences to the query sequence using heuristic algorithms. The tool is available on the NCBI website for web-based searching and also as a Standalone API.
The tool has many versions depending on the type of sequence. Nucleotide BLAST is for finding nucleotide-nucleotide sequences, blastx for translated nucleotide-protein sequences, tblastn for protein-translated nucleotide, and Protein BLAST for protein-protein sequences.
Many specialized searches can also be performed using it such as SmartBLAST, Primer-BLAST, Global Align, CD-search, IgBLAST, VecScreen, CDART, Multiple Alignment and MOLE-BLAST.
- It is an open source free to use
KEY FEATURES
- Different versions of BLAST are available depending on the type of query sequence
- Search performed by organism name, scientific name, taxonomy ID
- Customized filters for segregating results on different parameters
- Colorful graphical representation for similar regions
- The results can be used as input for other types of analysis
What Is Unique About BLAST?
A very easily available tool for a rough overview of the known/unknown organism sequence takes less time to show results.
Who BLAST Is Best For?
Computational biologists and Bioinformaticians can work with BLAST for preliminary research using any query sequence- protein or DNA.
21. QUAST
QUAST is a quality assessment tool for evaluating and comparing different genome assemblies by using better quality metrics and parameters. The tool is available for installation on local machines as well as available on web browsers for quick computations.
For comparisons, you can use a reference genome or evaluate without it too. It accepts multiple assemblies which is suitable for comparisons. The output files contain several formats- graphs, plots, and summaries that help scientists publish their work in highly reputed journals.
For guiding the users, evaluation demos are available for E.coli, H. sapiens and B.impatiens assemblies.
- It is an open source free to use
KEY FEATURES
- Evaluates genome assemblies in high quality and accuracy
- Interesting plots and graphs are available for quick summaries
- Publication-ready diagram available
- Computes the values with or without reference genomes
- Several versions and sub-types of QUAST are available such as- QUAST-LG, MetaQUAST
What Is Unique About QUAST?
QUAST can execute multiple assemblies for comparisons at once, without any errors for highly effective and positive results. Runs the algorithms without or with a reference genome.
Who QUAST Is Best For?
Any computational biologist dealing with genomes of unknown or known species can use the tool for quality assessment of genome assemblies.
22. Genome Analysis Toolkit
Genome Analysis Toolkit or GATK is developed by the Data Science platform at Broad Institute and offers a number of tools for variant discovery and genotyping. A very effective and powerful processing engine for high performance and computing of input files of any size.
Primarily focussed on variant discovery such as SNPs and indels in DNA and RNA-Seq data in germline. The tool also processes copy numbers and structural variation. GATK has several utilities to execute quality control of High-throughput sequencing data using other integrated tools.
Designed specifically for processing exomes and whole genomes produced by Illumina technology they also handle other technologies and experimental designs. Not just human genome data but any organism’s genome data is handled effectively by it.
- It is an open source free to use
KEY FEATURES
- The tool is optimized to produce the most accurate and high-quality results
- Utilizes the maximum computational efficiency for result generation
- Genomic analysis of exomes and whole genomes is possible
- Best practices workflows are offered for somatic short variants
What Is Unique About GATK?
The workflow recommendations offer the best practices to the users of GATK for highly optimized results of high quality.
Who GATK Is Best For?
For obtaining the best practices workflow, scientists and bioinformatics researchers can use GATK with ease.
23. FastTree
FastTree tool is used for phylogenetic analysis using maximum likelihood method for analysis. It can handle alignment for millions of sequences at maximum efficiency of time and memory. For large sequence alignments, it is faster than the other phylogenetic tools.
The users can download the code also for making any changes. At default settings, FastTree is more accurate than other platforms. It is much more accurate than the distance matrix methods used for large alignments.
The platform uses GTR generalised time-reversible models of nucleotide evolution and the JTT, WAG, and LG models of amino acid evolution. It uses a single rate for each site, and CAT approximation for varying evolution rates across sites. It computes local support values to estimate the reliability of every split in the tree.
- It is an open source free to use
KEY FEATURES
- It maintains only one topology at a time
- It considers only NNIs not SPR moves
- Optimises site rate categories and any model para metres only ones instead for each round
- Does not traverse into sub-stress that has no significant improvement in likelihood
What Is Unique About FastTree?
The platform works with five stages– Heuristic neighbourhood joining, reducing tree length, distance model, maximising tree likelihood, and local support values.
Who FastTree Is Best For?
Used by many Computational biology researchers for evolutionary studies by constructing maximum likelihood trees.
24. Harvest
Harvest is a core genome alignment and visualisation tool for the analysis of intraspecific microbial genomes. Created and maintained by the Centre for Bioinformatics and Computational Biology. Harvest is compatible with OSX and Linux platforms.
It has a fast core-genome multi-aligner called Parsnp and a dynamic platform for visualisation called Ginger. With the combination of both tools, interactive genome alignments, recombination detection and phylogenetic trees can be constructed.
- It is an open source free to use
KEY FEATURES
- The harvest platform has three components named harvest tools, Gingr & Parsnp
- Effective tool for quick analysis of intraspecific microbial genomes
- Experimental results for different species are available for reference
- The visualisation tool is interactive with a graphic user interface
What Is Unique About Harvest?
The input for harvest tools are binary format files and conversion utilities are available for conversion to different formats.
Who Harvest Is Best For?
Effective tool for SMP filtration, core genome phylogeny, and multiple core genome alignment hence suitable for microbiologists and computational biologist
25. MEGA
Molecular Evolutionary Genetics Analysis MEGA is a popular bioinformatics tool for evolutionary studies and analysis. It is compatible with Windows, Linux, MacOS, and similar platforms.
Different scopes for analysis (phylogeny, sequence alignment, model selection) are available using statistical methods (maximum likelihood, maximum parsimony, distance matrix) along with visualisation tools.
Online user manuals and example data are available for guidance to the new users. It has been cited by many recognised scientific publications. Publication-ready images are available with high quality. It offers cross-platform use with memory efficiency and a machine-learning framework.
- It is an open source free to use
KEY FEATURES
- Phylogeny inferences, model selection, and sequence alignment tools are available
- Statistical methods such as maximum likelihood, distance methods and maximum parsimony used
- Visualisation tools for alignment and tree generation are present
- Instructional videos are available on the usage of MEGA
What Is Unique About MEGA?
A wide range of phylogenetic tree construction is possible using any of the statistical methods in a very short time.
Who MEGA Is Best For?
Evolutionary biologists trying to draw evolutionary inferences for different groups of species can use the tool.
26. PathogenFinder
PathogenFinder is a web server tool for Bioinformatical purposes for the prediction of pathogenicity in bacteria by analysing the proteome, genome and raw reads produced by sequencing.
Platforms depend on groups of proteins formed without considering their annotated function or involvement in pathogenicity. Various customization settings are available before the execution of the processes.
The tool works with all the taxonomic groups of bacteria and uses the entire training set for analysis. The accuracy achieved so far is 88.6% on the independent test set.
- It is an open source free to use
KEY FEATURES
- The purpose of the tool is to identify and isolate the potential pathogenic organisms
- To identify the characteristics of both known and unknown strains of bacteria.
- The input file has reads obtained from next-generation sequencing platforms
- Assembled genome data is also used as an input file
What Is Unique About PathogenFinder?
This tool is effective during bacterial outbreaks for fast analysis of causal organisms for global epidemiology.
Who PathogenFinder Is Best For?
PathogenFinder is used globally by pathologists and medical microbiologists to identify deadly characters in pathogenic microbes.
27. ARIBA
Antimicrobial Resistance Identification By Assembly ARIBA, is a major tool for the detection of antimicrobial resistance. It identifies AMR-associated regions in the DNA and single nucleotide polymorphisms from short reads.
It generates very detailed output files that are customisable. The advantage of ARIBA over other tools is that it has high accuracy. The reference sequences in the AMR database are clustered by similarity using CD-HIT.
The platform requires reference sequences and SNP information for identifying resistance. It also supports various public resources and repositories that allow users to download data and easily convert it into different file formats.
- It is an open source free to use
KEY FEATURES
- Different versions of ARIBER are available such as ARG-ANNOT, VFDB, SRST2, CARD, and more
- Integrated with public repositories
- Allows data download and easy conversions
- Manipulation in output files is possible
- Code is available publicly for download and modification
What Is Unique About ARIBA?
Antimicrobial resistance increases threats for untreatable infections, hence ARIBA tool and its varied versions can resolve this issue by quick identification.
Who ARIBA Is Best For?
Drug discoverers and medical microbiology researchers can use the platform for malicious Gene and SNP identification.
28. SRST2
SRST2 is a tool based on Python language with major dependency on SAM tools and bowtie2. The tool achieves three major targets detecting genes, alleles, and multi-locus sequence types MLST.
It is developed to take Illumina sequence data as input, MLST database of gene sequences and identify the presence of STs and reference genes. It carries out mapping of short reads for executing these tasks.
For a good match, the fastq pair receives a number referring to the MLST allele combination it matches. A number and asterisk are received for small mismatches. Not found (NF) when no matching accuracy. Sometimes sequence pairs do not match and remain unrecognised and uncategorised.
- It is an open source free to use
KEY FEATURES
- The tool is robust and a great alternative for assembling the genomes by de novo methods
- Effective scoring system for quick analysis of reports
- Parallel runs and indexing is possible
- The whole genome sequence data or next-generation sequencing short reads data can be used
What Is Unique About SRST2?
Easy scoring method for categorizing the different sets of data. Good matches, small mismatches, and unmatched pairs are quick to identify.
Who SRST2 Is Best For?
SRST2 is a great tool for some basic initial analysis of read pairs obtained by next-generation sequencing, hence computational biologists can find it helpful
29. DNASTAR Lasergene
DNASTAR lasergene provides eight modules that comprise an overall system for sequence analysis. The tool is compatible with Windows, and macOS operating systems. Huge hard disk free space is needed for running the functions.
Various processes such as sequence quality improvement by trimming, assembly of sequence data, gene expression analysis, phylogenetic analysis, designing of primer, vector cloning, annotation and more can be executed.
The molecular biology package provides analysis for biomolecules, and the protein package is ideal for performing all protein-based searches and in-depth visualisation. The genomics package provides the next-generation sequencing analysis with an optimised user interface.
- It is commercial software with premium features on paid versions
>> Read DNASTAR Lasergene full Review
KEY FEATURES
- Provides high-quality research content through simplistic approaches
- Easy-to-use interface and outputs are publication-ready
- The cloning and designing of primers is available with the entire package
- Nova application for accurate prediction of protein models
What Is Unique About DNASTAR Lasergene?
The entire platform has three packages. Users have the flexibility to buy any individual product without any compulsions to buy the entire software.
Who DNASTAR Lasergene Is Best For?
The software can be used by any Bioinformatician belonging to a beginner or advanced category for sequence-based analysis of- proteins, DNA, and RNA.
30. SeqBuilder Pro
SeqBuilder Pro is a product by DNASTAR that performs very specific and well-defined tasks for macromolecular sequence analysis. The tool is compatible with Windows and macOS platforms with a hard disk requirement of at least 400 to 600 MB.
The tool has been cited several times in reputed journals and research papers. The tool is commercial and is available under different licenses for different sets of users. Users can go for the trial version before buying the product.
Video tutorials and user guides are available for guidance. Commendable user experience due to clear-cut division of the Control Panel.
- It is commercial software with premium features on paid versions
>> Read SeqBuilder Pro complete Review
KEY FEATURES
- It is a comprehensive software that allows the sequence of editing and manipulation
- Provides primer designing, mapping, annotation, and comparison of plasmids
- Simulated gel electrophoresis process is available
- Virtual cloning, accuracy and precision in output are commendable
- Publication-ready graphics and images generated as output
What Is Unique About SeqBuilder Pro?
It’s totally worth the price due to the high accuracy and quality of the results obtained at the end.
Who SeqBuilder Pro Is Best For?
Researchers belonging to the field of biotechnology and recombinant DNA technology can use the software
31. Sequencher
Sequencher tool developed by Gene Codes Corporation is helpful in the analysis of sequences obtained by NGS, Sanger sequencing and RNA-Seq. It is compatible with both Windows and macOS platforms. With certain specifications in hard disk and processor requirements, anyone can use it.
The tool is known for general analysis with customisation choices. It is connected with databases that helps in retrieving information from public repositories. The sequences from Sanger and NGS can be edited, trimmed, and assembled.
Multiple sequence alignment and SNP detection are available. Hundreds of scientific papers have been noticed for citing the tool. The tool is commercial with a free trial version for 15 days. Video tutorials and step-wise guides are available.
- It is commercial software with premium features on paid versions
>> Read Sequencher complete Review
KEY FEATURES
- General and in-depth analysis of reads obtained via sequencing methods
- Public repositories and databases are integrated with the tool
- Easy retrieval of data files from different sources, various output formats available
- Fast and accurate results with optimised use of algorithms
- Flexibility in the choice of settings for parameters
What Is Unique About Sequencher?
Flexibility in the choice for buying a licence according to the needs of an individual. One can go for a standalone, shared network or institution license.
Who Sequencher Is Best For?
Advanced researchers working on short reads and mapping of next-generation sequencing data can take advantage of this
32. Geneious
Geneious is one of the best Bioinformatics tools and is a popular tool due to its cost-effectiveness and results generation. The software is created using Java. It is supported by Windows, Linux and Mac platforms.
It offers several biological analysis features such as manipulation and visualisation of sequences, sequence alignment, and phylogenetic analysis. The next-generation sequencing data can be assembled and analysed. The three-dimensional structures can be labelled and annotated.
The assembly and editing of chromatograms is present. Alignments and phylogenetics are done using accurate algorithms. Since the software is commercial, different subscription options are available. A free trial version of 14 days will let you explore the features.
- It is commercial software with premium features on paid versions
>> Read Geneious complete Review
KEY FEATURES
- A user-friendly tool to carry out essential genomic analysis.
- Helps in the import and export of sequences and annotation
- Automatic workflows are available with database integrity
- Simple primer designing and cloning options
What Is Unique About Geneious?
Several genomic tools are embedded for NGS, Sanger, long read and different data source sequence analysis
Who Geneious Is Best For?
Automatic workflows make the execution easy hence handy tool for researchers with heavy data for analysis
33. CLC Workbench
CLC Main Workbench is known for the thousands of scientific research it has executed ranging from proteins to DNA. An all-rounder package for thorough analysis of sequences, it’s editing and visualisation on suitable tools.
It is compatible with Windows macOS and Linux platforms with Java runtime environment. Very well-categorised user interface for friendly user experiences. Customer support and user manuals are available for beginners. A 14-day free trial version is available before buying the actual package.
- It is commercial software with premium features on paid versions
>> Read CLC Main Workbench complete Review
KEY FEATURES
- The 3-D viewer Allows visualisation of 3-D coordinates of PDB files.
- Evolutionary relationships can be drawn between different organisms
- General analysis for a quick overview
- Nucleotide and protein manipulations and analysis are available
- Cloning and restriction site detection
- Prediction of RNA structure is feasible
What Is Unique About CLC Workbench?
It includes most of the functional analysis possible for different biomolecules. Integration of plug-ins is possible for workbenches via open API.
Who CLC Workbench Is Best For?
Most of the sequence and structural analysis for different biomolecules can be executed with the workbench hence suitable for computational biologists.
34. SnapGene
SnapGene executes the task in three steps: planning, visualisation and documentation. Several robust features make the tool extraordinary and popular among the research community.
Perform certain basic analyses of sequence alignment, visualisation using viewer software, editing and annotations, molecular cloning, development of primers and more.
Some other essential functions are performing virtual PCR and mutagenesis, agarose gel simulation, and translation into proteins.
It also offers easy file conversion into different formats. Flawless user experience due to simple click interface. Several subscription choices are available with the 30-day free trial before subscribing.
- It is commercial software with premium features on paid versions
>> Read SnapGene complete Review
KEY FEATURES
- High citation numbers and accurate results
- Effective management of data, import and export of files
- Easy search and detection of regions in DNA and protein sequences
- Graphical history is available along with the undo option
What Is Unique About SnapGene?
Commercial software with elaborate and extensiveness such as providing a step process for cloning.
Who SnapGene Is Best For?
Computational biologists, Corporations, academic professionals and software programmers can find the tool handy in various interdisciplinary fields of science
Free vs Commercial Bioinformatics Software, Which One Should You Go For?
This is an endless vicious debate about which one to go for. Choosing between free and commercial software is not a feasible choice for a researcher. When it comes to productive research results, we recommend you go for the most accurate bioinformatical tools.
Sometimes the precise results can be obtained only through paid software that uses heavy computational powers for analysis. Often, free and open-source software gives optimum results that any paid software could give. For example- AutoDock is the most cited docking software, it is open-source and freely available for use.
The purpose of the research can be met with either of the two- free or commercial bioinformatical software. We would not recommend you to rigidly choose between them. You can go for the software that you think might be most appropriate to meet your needs.
How to Choose Best Bioinformatics Software for Your Research?
Out of several outstanding choices, picking programs for a specific job can be a tough decision. Here are a few highlights to keep in mind before finalizing a tool for research activities.
- Know your need– Identify your exact requirements for research. Understand the goal of doing the analysis work, like what you want to obtain as an output.
- Understand the tool– Fully crosscheck the features of a tool to understand its purpose before using it.
- Check your budget– Choose free software if you are working on a daily based small-level project. Go for paid ones when you are financially supported and doing high-grade work.
- Do not rush– Do not run for the paid versions only because everyone else is doing it. Not every paid software is worth the price.
- Scientifically sound & accurate– Choose the tools that most of the researchers have already used for analysis in their published work. Most cited tools are expected to be scientifically accurate.
Which is The Best Bioinformatics Software for a Beginner?
EMBOSS, Clustal, and MEGA are some of the reliable tools to learn bioinformatical analysis if you happen to be a beginner. The tools are simplistic and customizable. It has a simple user interface and processing time is also less.
Besides them, you can us several small and specific task tools available at the National Center for Biotechnology Information.
Which Software is Best for Sequence Analysis?
If you wish to work on an open source that is freely available to use, go for EMBOSS. Otherwise, several commercial software are available too for publication-ready results such as DNASTAR Lasergene and Geneious.
National Center for Biotechnology Information also supports some basic tools such as BLAST and its varied versions for different types of input sequences.
In this elaborate article, we have focussed on the 30+ Best Bioinformatics Software and tools available for computational analysis of high throughput biological data and basic bioinformatical operations. This is a random list and does not indicate any rankings.
According to us, each of the tools defined are popular bioinformatics tools in their field of analysis. As an enthusiastic Bioinformatician or Computational Biologist, you would find them highly effective, fast and accurate in results production.
You can add to this list or eliminate it according to your user-friendliness and awareness. After thoroughly reviewing them, use your customized pipeline for in-depth research on macromolecules.
Helpful Software for Bioinformatic Industry