DECODE The Script of LIFE

Are you looking forward to making some phenomenal contribution to the field of medical sciences using computational skills? Then you are at the right spot at the right time. Today we shall discuss about 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 into 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. But 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 tool that is globally recognized and used for analysis.

1. GALAXY

GALAXY is a popular bioinformatics tool extensively used for data integration, 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 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 to 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.

Step-by-step tutorial is provided for beginners to learn molecular modelling from scratch. It can be used for the 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 does not affect.

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 of the ligand to set of grids of the target protein. The second part is for pre-calculating the grids.

The software works on sophisticated gradient optimisation method and calculation of 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 discovery of drugs including HIV1 integrase inhibitors.

4. BioJava

BioJava is a bioinformatical platform dedicated for processing diverse biological data using Java tools. Written in Java language, it is compatible on the web browser platform with Java run environment.

Various operations such as sequence manipulation, protein structure analysis, Distributed Annotation System (DAS), dynamic programming, Common Object Request Broker Architecture (CORBA) interoperability are performed.

Projects accomplished using BioJava platform- Strap, Geneious, GenBeans, Cytoscape, Bioclipse and more. Modify BioJava from 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 an 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 analysis of genomic data.

Who BioJava Is Best For?

Many renowned bioinformatics projects have been accomplished using BioJava. An ideal tool for core computational biologist.

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 copy, accurate bacterial taxonomic composition of metagenomic shotgun sequencing data can be inferred by employing AMPHORA2.

AmphoraVizu is a web server platform that allows to visualize 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 it on 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. The 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 users community.

More than 200 applications for molecular analysis and basic bioinformatics operations available. Sequence alignment, database searching, protein motif identification, domain analysis and much more is available.

It has C programming libraries with powerful API. Many inbuilt functionalities and convenient platform. Many interfaces 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 that enables powerful workflow for constructing pipelines

Who EMBOSS Is Best For?

Includes different type of analysis packages hence any biological/computational researcher can use EMBOSS for specific type 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, Windows operating systems.

This tool is fast and reliable for visualising the vast data on desktop. It loads local files as input from 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 that 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 map are some of the distinct visualisation formats that makes it unique from similar tools.

Who Integrated Genome Browser Is Best For?

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, 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 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 basic understanding of the command language in R programming. Without expertise knowledge in programming, biologist can analyse data.

Who Bioconductor Is Best For?

Bioconductor packages having strong computing facilities can be used by data biologist 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 includes methods, parameters, data usage, and result generation.

GenePattern repository is created for discussion on modules 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 user to share and understand 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 reads sequencing and flow cytometry
Users can create account, perform analysis, create pipelines and save
Multiple interfaces available as web browsers, application, 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 biologist 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 on Windows, Linux, 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 provides 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 available

What Is Unique About Geworkbench?

Allows integration with third-party tools such as cytoscape, genomespace and genepattern 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 available

11. GROMACS

GROMACS is a versatile package to perform molecular dynamics and simulations. It is compatible with Linux, Windows, macOS and other UNIX variety. It is one of the popular bioinformatics tool available for worldwide researches.

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 in the tool for extended simulation process 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 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 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 and 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 more similar operating systems.

The entire package of Clustal has several tools integrated into it. ClustalV, ClustalW, Clustal Omega are few of them. Clustal 2/Clustal X is also known popularly for 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 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
Wide range of input files accepted- FASTA, NBRF, PIR, EMBL, GDE, RSF, GCC, Clustal and more
Output format 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 degree 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 browser.

Compatible with Windows, Linux, macOS platforms. The tool provides simple method to control quality checks of raw data coming directly from sequencing pipelines. Manual guides 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 about 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 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?

Microbiologist and virologists can take advantage from 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 are 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 while 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 lose little information during the process.

Who Velvet Is Best For?

Velvet can be used by computational biologists and bioinformaticians for assessing very short read 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 perform 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 by 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, 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 machine learning approach
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) tool is 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 need 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 genome from different organisms. This involves three major algorithms called BWA backtrack, BWA-SW, and BWA-MEM.

For longer Illumina sequence read, BWA backtrack algorithm is used. For longer sequences other two algorithms are widely used. Each of the algorithms are 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 high quality and accuracy
Fast and accurate methods for alignment of long reads from different sequencers
Long reads are smoothly aligned with 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 variation 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 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 fasta file that contains improved representation of the genome and VCF detailing variations between reads and input genome file.

It is an open source free to use

KEY FEATURES

Various input and output file formats are available
Manual inspection and editing is allowed for better results
Major improvements in the input genome can be made
Changes can be viewed in 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 upon microbial and viral genomes can use the tool for identifying variations between the reference genomes and query sequence.

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 Standalone and 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 available depending on 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 similarity regions
The results can be used as input for other type of analysis

What Is Unique About BLAST?

A very easily available tool for a rough overview on the known/unknown organism sequence, takes less time for showing 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 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 browser 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, summaries that helps scientists in publishing their work at 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 is 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 Data Science platform at Broad Institute offer 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 number 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 but they also handle other technologies and experimental designs. Not just human genome data but any organisms genome data is handled effectively by it.

It is an open source free to use

KEY FEATURES

The tool is optimized to produce most accurate and high quality results
Utilizes the maximum computational efficiency for result generation
Genomic analysis of exomes and whole genomes are 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, LG models of amino acid evolution. It uses single rate for each site, CAT approximation for varying evolution rates across sites. It computes local support values to estimate 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 to traverse into sub stress that have 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 analysis of intraspecific microbial genomes. Created and maintained by Centre for bioinformatics and computational biology. Harvest is compatible with OSX and Linux platforms.

It has a fast core genome multi-a ligner called Parsnp and a dynamic platform for visualisation called Gingr. With the combination of both the 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 analyzation of intraspecific microbial genomes
Experimental results for different species is available for reference
The visualisation tool is interactive with 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 microbiologist 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 manual and example data is 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 machine learning framework.

It is an open source free to use

KEY FEATURES

Phylogeny inferences, model selection, sequence alignment tools are available
Statistical methods such as maximum likelihood, distance methods and maximum parsimony used
Visualisation tools for alignment, tree generation is present
Instructional videos are available on usage of MEGA

What Is Unique About MEGA?

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 group of species can use the tool.

26. PathogenFinder

PathogenFinder is a web server tool for Bioinformatical purpose for the prediction of pathogenicity in bacteria by analysing the proteome, genome and raw reads produced by sequencing.

Platforms depends on groups of proteins formed without considering their annotated function or involvement in pathogenicity. Various customization settings are available before 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 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 genomes data is also used as 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 the pathologists and medical microbiologist to identify deadly characters in pathogenic microbes.

27. ARIBA

Antimicrobial Resistance Identification By Assembly ARIBA, is a major tool for 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 advantages 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 allows users to download data and easily convert it in different file formats.

It is an open source free to use

KEY FEATURES

Different versions of ARIBER 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 of 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 is received for small mismatch. Not found (NF) when no matching accuracy. Sometimes sequence pair 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 set of data. Good match, small mismatch, 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, 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, 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 optimised user interface.

It is a commercial software with premium features on paid versions

>> Read DNASTAR Lasergene full Review

KEY FEATURES

Provides high quality research content by 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 beginner or advance category for sequence based analysis of- proteins, DNA, and RNA.

30. SeqBuilder Pro

SeqBuilder Pro is a product by DNASTAR performs very specific and well-defined tasks for macromolecular sequence analysis. The tool is compatible with Windows and macOS platforms with 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 set 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 Control Panel.

It is a commercial software with premium features on paid versions

>> Read SeqBuilder Pro complete Review

KEY FEATURES

It is a comprehensive software allowing 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 is commendable
Publication ready graphics and images generated as output

What Is Unique About SeqBuilder Pro?

It’s totally worth the price due to 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 analysis of sequences obtained by NGS, Sanger sequencing and RNA-Seq. It is compatible with both Windows and macOS platform. With certain specifications in hard disk and processor requirement, 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, assembled.

Multiple sequence alignment and SNP detection is available. Hundreds of scientific papers have been noticed for citing the tool. The tool is commercial with free trial version for 15 days. Video tutorials and step wise guide available.

It is a 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 database 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 choice of settings for parameters

What Is Unique About Sequencher?

Flexibility in the choice for buying licence according to the needs of individual. One can go for standalone, shared network or institution license.

Who Sequencher Is Best For?

Advance researchers working on short reads and mapping of next-generation sequencing data can take advantage from this

32. Geneious

Geneious is one of the best Bioinformatics tools and 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 chromatogram 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 a 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 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 thousands of scientific researches 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, user manual are available for beginners. 14 days free trial version available before buying the actual package.

It is a 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 available
Cloning and restriction sites 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 work benches 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 biologist.

34. SnapGene

SnapGene execute the task in three steps that is planning, visualisation and documentation. Several robust features makes the tool extraordinary and popular among the research community.

Perform certain basic analysis 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 Days free trial before subscribing.

It is a commercial software with premium features on paid versions

>> Read SnapGene complete Review

KEY FEATURES

High citations number 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 undo option

What Is Unique About SnapGene?

A commercial software with elaborate and extensiveness such as providing one step process for cloning.

Who SnapGene Is Best For?

Computational biologists, Corporates, 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 for which one to go for. Choosing between free and commercial software is not a feasible choice as a researcher. When it comes to productive research results, we recommend you to go for most accurate bioinformatical tools.

Sometimes the precise results can be obtained only through a paid software that uses heavy computational powers for analysis. Often, the free and open source software give 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 a research. Understand the goal of doing the analysis work, like what do 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 a 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, 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 simple user interface and processing time is also less.

Besides them, you can us several small and specific task tools available on 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 up to this list or eliminate according to your user-friendliness and awareness. After thoroughly reviewing them, use your customized