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http://www.ebi.ac.uk/Tools/msa/muscle/
Multiple sequence alignment method with reduced time and space complexity.Multiple sequence alignment with high accuracy and high throughput. Data analysis service for multiple sequence comparison by log- expectation.
Proper citation: MUSCLE (RRID:SCR_011812) Copy
http://www.clcbio.com/products/clc-genomics-workbench/
Commercially available software for visualization and analysis of next generation sequencing data. Used for viewing, exploring, and sharing of NGS analysis results. Complete toolkit for genomics, transcriptomics, epigenomics, and metagenomics in one program.
Proper citation: CLC Genomics Workbench (RRID:SCR_011853) Copy
Modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for the analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM) and it supports a lot of SPM data formats. However, it can be used for general height field and (greyscale) image processing, for instance for the analysis of profilometry data or thickness maps from imaging spectrophotometry.
Proper citation: Gwyddion (RRID:SCR_015583) Copy
https://omictools.com/dog-picker-tool
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software tool for general particle picking in the single-particle processing of unknown macromolecules. Reference free particle picker with ability to sort particles based on size or it can be used to bootstrap the creation of templates or training datasets for other particle pickers. Used to facilitate particle selection in single particle electron microscopy., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: DoG picker (RRID:SCR_016655) Copy
https://github.com/davidemms/OrthoFinder
Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format.
Proper citation: OrthoFinder (RRID:SCR_017118) Copy
https://www.bioconductor.org/packages/release/bioc/html/MetaNeighbor.html
Software package to assess cell type identity using both functional and random gene sets. Used for single cell replicability analysis to quantify cell type replicability across datasets using neighbor voting.
Proper citation: MetaNeighbor (RRID:SCR_016727) Copy
https://github.com/csb-toolbox/CSB
Software package as an application framework and a Python class library. It is designed for reading, storing and analyzing biomolecular structures in a variety of formats with rich support for statistical analyses.
Proper citation: Computational Structural Biology Toolbox (RRID:SCR_016065) Copy
http://www.premierbiosoft.com/dnamicroarray/index.html
Oligo and cDNA Microarray Design Software that designs thousands of primers and probes for oligo and cDNA microarrays in seconds.
Proper citation: Array Designer (RRID:SCR_010960) Copy
Powerful, accessible statistical tools for fast visualization and analysis of microarrays - expression arrays, miRNA, exon arrays and genomics copy number data.
Proper citation: GeneSpring GX (RRID:SCR_010972) Copy
http://www.exiqon.com/mirna-array-software
Software for fast and accurate analysis of miRCURY LNA microRNA Array data.
Proper citation: miRCURY LNA microRNA Array Analysis Software (RRID:SCR_010952) Copy
http://realtimegenomics.com/products/variant-1.0
The product line encompasses distinct products for the specific needs of clinical research, saving time and money while allowing customers to focus on the answers they need most.
Proper citation: RTG Variant (RRID:SCR_010805) Copy
http://realtimegenomics.com/products/metagenomics-1.0
Delivers comprehensive shotgun metagenomics sequence analysis for accurate species frequency composition and protein searching.
Proper citation: RTG Metagenomics (RRID:SCR_011949) Copy
http://www.genomatix.de/solutions/index.html
With their unique combination of proprietary algorithms and comprehensive data background, all our solutions do more than enable you to efficiently and effectively analyze and interpret biological data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Genomatix Solutions (RRID:SCR_011855) Copy
http://sbcb.bioch.ox.ac.uk/kdb/
A Database of Potassium Ion Channel Homology Models & Molecular Dynamics Simulations.
Proper citation: Potassium Channel Database (RRID:SCR_011960) Copy
A phylogenetic tree of global human mitochondrial DNA variation, based on both coding- and control-region mutations, and including haplogroup nomenclature.
Proper citation: PhyloTree.org (RRID:SCR_012948) Copy
http://www.meta-analysis.com/index.php
A software package to do meta-analysis which works in a spreadsheet interface and also provides forest plots, which are useful for visualizing between-study heterogeneity.
Proper citation: CMA (RRID:SCR_012779) Copy
http://www.ebi.ac.uk/ena/search/
A nucleotide sequence similiary search tool which is far faster than BLAST for large datasets, with only a marginal loss in search sensitivity.
Proper citation: ENA Sequence Search (RRID:SCR_013170) Copy
http://jbirc.jbic.or.jp/h-dbas/
A specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. H-DBAS offers unique data and viewer for human Alternative Splicing (AS) analysis. It contains: * Genome-wide representative alternative splicing variants (RASVs) identified from following datasets * H-Inv full-length cDNAs (resource summary): H-Invitational cDNA dataset * H-Inv all transcripts (resource summary): Published human mRNA dataset * Mouse full-length cDNAs (resource summary): Mouse cDNA dataset * RASVs affecting protein functions such as protein motif, GO, subcellular localization signal and transmembrane domain * Conserved RASVs compared with mouse genome and the full-length cDNAs (H-Inv full-length cDNAs only)
Proper citation: Human Transcriptome Database for Alternative Splicing (RRID:SCR_013305) Copy
Blog including established profound know-how and proprietary protocols to cover a broad range of applications.
Proper citation: NGS Expert Blog (RRID:SCR_013218) Copy
http://zope.bioinfo.cnio.es/plan2l/plan2l.html
A web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. The system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned.
Proper citation: PLAN2L (RRID:SCR_013346) Copy
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