Best Bioinformatics Software for Linux of 2024

OmicsBox, a leading bioinformatics tool, offers end-toend data analysis for genomes, transcriptomes and metagenomes. It also provides genetic variation studies. The application, which is used by leading private and public research institutes worldwide, allows researchers to process large and complicated data sets and streamline their analytical process. It is designed to be efficient, user-friendly and equipped with powerful tools to extract biological insight from omics data. The software is divided into modules, each of which has a set of tools and features designed to perform specific types of analyses, such as de novo genome assemblies, genetic variations analysis, differential expression analyses, taxonomic classifications, and taxonomic classes of microbiome, including the interpretation of results and rich visualizations. The functional analysis module uses the popular Blast2GO annotating methodology, making OmicsBox a great tool for non-model organisms research.

Interactive visualizations and analytics allow you to explore hundreds of single-cell transcriptome datasets as well as your own data. The software supports multimodal omics (e.g. CITE-seq and spatial transcriptomic. Explore the world's largest database of single-cell expression interactively. Access and query insights derived from a single cell database of millions of cells. The database is fully annotated, with cell type labels and experimental meta-data. BBrowser does not just create a portal to published works. It is an end-toend solution for YOUR single-cell data. Import your fastq, count matrices or Seurat objects and reveal the biological stories within. With a powerful package of visualizations, analyses and an intuitive interface you can easily mine insights from any single-cell dataset. Import data from single-cell CRISPR or Perturb-seq. Guide RNA sequences can be queried.

Ruffus is a Python computation pipeline library. It is open-sourced and powerful, user-friendly, and widely used for science and bioinformatics. Ruffus was designed to automate scientific and other analyses with minimal fuss and effort. It is suitable for even the most basic tasks. Even complex pipelines can be handled. This will prevent make or scons from becoming cross-eyed and recursive. No "clever magic", no pre-processing. The lightweight syntax, which does one small thing well, is unambitious. Ruffus is licensed under the permissive MIT-free software license. This license allows for free use and inclusion in proprietary software. It is a good idea to run your pipeline in a temporary directory that is not connected to your original data. Ruffus is a lightweight Python module that can be used to build computational pipelines. Ruffus requires Python 2.6 and higher, or Python 3.0 and higher.

Geneious Prime makes bioinformatics more accessible by transforming raw information into visualizations which make sequence analysis intuitive. Simple assembly of sequences and easy editing contigs. Automatic annotation of gene prediction, motifs and translation. Genotype microsatellite trace with automated ladder fitting, peak calling, and generation of tables of alleles. A highly customizable sequence view displays beautiful visualizations of annotated assemblies and genomes. SNP variants analysis with powerful SNPs, RNA-Seq analysis and amplicon metagenomics. Create your own searchable database of primers for PCR and sequencing and design and test them. Geneious Biologics offers a flexible, scalable and secure way to streamline antibody analysis workflows. It allows you to create high-quality libraries, and select the best therapeutic candidates.

The toolkit was developed in the Data Sciences Platform of the Broad Institute. It offers a variety of tools, with a focus on variant detection and genotyping. Its powerful processing engine, high-performance computing capabilities and flexibility make it a great tool for any project. The GATK is a standard in the industry for identifying SNPs in RNAseq and germline DNA data. Its scope has now expanded to include somatic short variation calling, copy number (CNV), and structural variation (SV). The GATK includes not only the variant callers, but also many utilities that perform related tasks like processing and quality-control of high-throughput sequence data. It also bundles the Picard toolkit. These tools were designed primarily to process whole genomes and exomes generated by Illumina sequencing technology. However, they can be adapted for a variety other technologies and experimental design.

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulatory in RNA-Seq sample. It accepts aligned RNA Sequence reads and assembles them into a minimal set of transcripts. Cufflinks estimates the relative abundances for these transcripts by calculating how many reads each one receives, while taking into account biases from library preparation protocols. Cufflinks is the result of a collaboration between the Laboratory for Mathematical and Computational Biology. We provide binary packages for Cufflinks to make the installation process easier. This saves users the sometimes frustrating task of building Cufflinks which requires you to install the libraries. Cufflinks comes with a number tools for analyzing RNASeq experiments. Some of these tools are standalone, while others form part of a larger workflow.

The Bioconductor Project aims to develop open source software that allows for repeatable and precise analysis of biological data. We encourage a collaborative and inclusive community of data scientists and developers. Resources to maximize Bioconductor's potential. Our tutorials, guides, documentation, and guides cover everything from basic functionality to advanced features. Bioconductor is an open-source and open-development software that uses the R statistical language. It has an active user base and two releases per year. Bioconductor offers Docker images with every release, and supports Bioconductor in AnVIL. Bioconductor, founded in 2001, is an open-source project widely used in bioinformatics. Over 1,000 developers have contributed over 2,000 R packages, which are downloaded over 40 million times per year. Bioconductor is cited in over 60,000 scientific publications.

This free tool provides stunning visualizations of genomic data, giving you the power to see exactly what is happening at each base pair within your samples. GenomeBrowse is a desktop application that runs natively on your computer. You no longer have to compromise on speed or interface quality in order to achieve a consistent experience across platforms. It was designed with performance in mind, to provide a faster browsing experience than any genome browser currently available. GenomeBrowse has also been integrated into the powerful Golden Helix VarSeq annotation and interpretation platform. VarSeq is a powerful tool for filtering, analyzing, and annotating your data. If you enjoy the visualization experience provided by GenomeBrowse then try it out. GB can show all your alignment data. You can find context-relevant findings by looking at all your samples together.

MEGA (Molecular Evolutionary Genetics Analysis), a powerful, user-friendly software package designed to analyze DNA and protein sequences from species and populations. It allows for both manual and automatic sequence alignment, phylogenetic trees inference, and evolutionary hypotheses testing. MEGA is a powerful tool for comparative analysis of sequences and understanding molecular evolutionary processes. It supports a wide range of statistical methods, including maximum likelihood, Bayesian Inference, and ordinary least-squares. MEGA has advanced features like real-time captions to explain the results of the analysis and the methods used. It also uses the maximum composite likelihood method to estimate evolutionary distances. The software comes with powerful visual tools such as the alignment/trace editors and tree explorers, and supports multi-threading to ensure efficient processing. MEGA is compatible with Windows, Linux and macOS.

StarDrop™, a comprehensive suite of integrated software, delivers the best in silico technology within a highly visual interface. StarDrop™, which allows seamless flow between the latest data, predictive modeling, and decision-making regarding the next round or synthesis, improves the speed, efficiency and productivity of the discovery process. A balance of different properties is essential for successful compounds. StarDrop™, which guides you through the multi-parameter optimization challenge, helps you target compounds with the highest chance of success. It also saves you time and resources by allowing you to synthesize fewer compounds and test them less often.

Swiss-PdbViewer, also known as DeepView, is an application that allows you to analyze multiple proteins simultaneously. To compare active sites and other parts, the proteins can be superimposed. The intuitive interface and graphic make it easy to find information about amino acid mutations, Hbonds, angles and distances between atoms. Nicolas Guex has been developing Swiss-PdbViewer (aka DeepView), since 1994. Swiss-PdbViewer was originally tightly connected to SWISS-MODEL (an automated homology modeling server) that was developed at the Structural Bioinformatics Group of the Biozentrum in Basel. The SWISS-MODEL interface has evolved to the point that advanced modeling can now be done directly. It is no longer possible to maintain a direct interface with SwissPdbViewer.

Avogadro, an advanced molecule editor/visualizer, is designed for cross-platform usage in computational chemistry and molecular modeling. It provides high-quality rendering and a powerful plugin structure. Avogadro, a free and open-source molecular editor/visualization tool, is available for Mac, Windows, and Linux. It can be used in computational chemistry and molecular modeling as well as materials science and other related areas. It provides flexible, high-quality rendering and a powerful plugin structure.

Loupe Browser is an intuitive visualization software that allows you to explore and analyze 10x Genomics Chromium or Visium data. LoupeR can convert Seurat objects to Loupe Browser files. The Loupe Browser interface's navigation and interactive features are based on a dataset of lung squamous-cell carcinoma. The workspace is centered on the view panel, where single points representing barcodes of cells are shown in different projections. Each point represents a barcode. The vast majority of them correspond to a cell. The default projection, created by the Cell Ranger pipeline, is the tSNE plot. Other projections are also available. You can move the plot by dragging the mouse over cells. Zoom in and out using the mouse wheel or trackpad. Cluster labels will appear as you move the mouse over the plot. This is useful for data with a large number of precomputed groups.

Choose two custom cell groups and compare their top differentially-expressed genes. Use millions of cells in the integrated CZ CELLxGENE Corpus for powerful analyses. Use an interactive, no-code interface to perform interactive analyses of a dataset. Explore how spatial, environmental and genetic factors influence gene expression patterns. Use published datasets to understand them or as a starting point for identifying new cell subtypes and states. Census allows you to access any custom slice of standard cell data from CZ CELLxGENE in R or Python. Explore an interactive encyclopedia that contains 700+ cell types, detailed definitions, markers genes, lineage and relevant datasets. Browse and download 1,000+ datasets and hundreds of standardized data sets that characterize the functionality of healthy human and mouse tissues.