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http://toolkit.tuebingen.mpg.de/

A platform that integrates a great variety of tools for protein sequence analysis. Many tools are developed in-house, and serveral public tools are offered with extended functionality. Most frequently used tools HHpred Sensitive protein homology detection and structure prediction by HMM-HMM-comparison. Starting from a query sequence, HHpred builds a multiple sequence alignment using HHblits and turns it into a profile HMM. This is then compared it with a database of HMMs representing proteins with known structure (e.g. PDB, SCOP) or annotated protein families (e.g. PFAM, SMART, CDD, COGs, KOGs). The output is a list of closest homologs with alignments. HHpred can also build 3d homology models using the identified templates in the PDB database. It can optimize template picking and query-template alignments for homology modeling. The HHblits software is part of the open source package HHsuite. HHblits Remote homology detection method based on iterative HMM-HMM comparison. HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and iteratively searches through uniprot20 or nr20 databases by adding significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments. The HHblits software is part of the open source package HHsuite. Quick2d Quick2D gives you an overview of secondary structure features like alpha-helices, extended beta-sheets, coiled coils, transmembrane helices and disorder regions. Predictions by PSIPRED, JNET, Prof(Rost), Prof(Ouali), Coils, MEMSAT2, HMMTOP, DISOPRED2 and VSL2. Modeller A Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Coils/PCoils This server compares a single sequence (COILS) or a sequence alignment (PCOILS) to a database of known coiled-coils and derives a similarity score. The program then calculates the probability that the sequence will adopt a coiled-coil conformation. PSI-Blast Search with an amino acid sequence against protein databases for locally similar sequences. Similar to ProteinBLAST but more sensitive. PSI-BLAST first performs a BLAST search and builds an alignment from the best local hits. This alignment is then used as a query for the next round of search. After each successive round the search alignment is updated.

Proper citation: Bioinformatics Toolkit (RRID:SCR_010277) Copy   

•   Source: SciCrunch Registry

http://pipeline.lbl.gov/cgi-bin/gateway2

Software tools for comparative genomics.Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.

Proper citation: VISTA Browser (RRID:SCR_011808) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/htqc/

A software toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc..

Proper citation: HTQC (RRID:SCR_006448) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/alkesgroup/Eagle/

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

Proper citation: Eagle (RRID:SCR_015991) Copy   

•   Source: SciCrunch Registry

https://github.com/theislab/scvelo

Software package for estimating and analyzing RNA velocities in single cells using dynamical modeling. RNA Velocity using dynamical modeling.

Proper citation: scVelo (RRID:SCR_018168) Copy   

•   Source: SciCrunch Registry

https://www.gnu.org/software/octave/

A high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments. It may also be used as a batch-oriented language. Octave has extensive tools for solving common numerical linear algebra problems, finding the roots of nonlinear equations, functions written in the Octave language, or by using dynamically loaded modules written in C, C++, Fortran, or other languages., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GNU Octave (RRID:SCR_014398) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/topGO.html

Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.

Proper citation: topGO (RRID:SCR_014798) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/danposdoc/

Software toolkit with various functions for the analysis of nucleosome and protein occupancy by sequencing.

Proper citation: DANPOS2 (RRID:SCR_015527) Copy   

•   Source: SciCrunch Registry

https://github.com/HASTE-project

Software toolkit for rapid development of cloud native intelligent data pipelines for scientific data streams. Hierarchical approach to acquisition, analysis, and interpretation of image data. Developed in the project Hierarchical Analysis of Spatial and Temporal Data.

Proper citation: HASTE-project (RRID:SCR_020932) Copy   

•   Source: SciCrunch Registry

https://mermaid.readthedocs.io/en/latest/

Registration toolbox written in pyTorch. Supports various image registration methods. Focuses on nonparametric registration approaches including stationary velocity fields and large discplacement diffeomorphic metric mapping models though simple affine registration is also possible. Allows for rapid prototyping of new image registration approaches and similarity measures.

Proper citation: MERMAID (RRID:SCR_020939) Copy   

•   Source: SciCrunch Registry

https://github.com/Ecogenomics/GtdbTk

Open source software tool for assigning objective taxonomic classifications to bacterial and archaeal genomes based on Genome Database Taxonomy. Designed to work with recent advances that allow metagenome assembled genomes to be obtained directly from environmental samples. Can also be applied to isolate and single cell genomes.

Proper citation: GTDB-Tk (RRID:SCR_019136) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/ensembldb.html

Software R package to create and use Ensembl based annotation resources.

Proper citation: ensembldb (RRID:SCR_019103) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/biomerieux-data-science/clustlasso

Software R package to build predictive signatures of microbial phenotypes. Software package implementing cluster lasso approach.

Proper citation: clustLasso (RRID:SCR_018820) Copy   

•   Source: SciCrunch Registry

https://github.com/big-data-lab-team/spot

Open source software tool for file based localization of numerical perturbations in data analysis pipelines. Identifies components in pipeline, at resolution level of system process, that produce different results in different execution conditions.

Proper citation: Spot (RRID:SCR_018915) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/GALLO/vignettes/GALLO.html

Software R package developed for accurate annotation of genes and quantitative trait loci located in regions identified in common genomic analyses performed in livestock, such as Genome Wide Association Studies and transcriptomics using RNA-Sequencing. Allows graphical visualization of gene and QTL annotation results, data comparison among different grouping factors like methods, breeds, tissues, statistical models, studies and QTL enrichment in different livestock species including cattle, pigs, sheep, and chickens.

Proper citation: Genomic Annotation in Livestock for positional candidate LOci (RRID:SCR_019212) Copy   

•   Source: SciCrunch Registry

https://github.com/SMI/SmiServices

Software suite of tools for cataloguing and anonymising DICOM files, as used for Scottish Medical Imaging project. Software suite of microservices for loading, anonymising, linking and extracting large volumnes of dicom medical images to support medical research. Platform allows dicom tags extracted from clinical images to be loaded into MongoDB and relational database tables for purposes of generating anonymous linked research extracts including image anonymisation.

Proper citation: SMI Services (RRID:SCR_018881) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=psych

Software R package for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis.Procedures for Psychological, Psychometric, and Personality Research. Used for personality, psychometric theory and experimental psychology.

Proper citation: psych (RRID:SCR_021744) Copy   

•   Source: SciCrunch Registry

http://solexaqa.sourceforge.net/

Software package to calculate sequence quality statistics and create visual representations of data quality for Illumina's second-generation sequencing technology.

Proper citation: SolexaQA (RRID:SCR_005421) Copy   

•   Source: SciCrunch Registry

http://phast.wishartlab.com/

A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage cornerstone feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage quality and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. Databases available for download include Virus DB, Prophage and virus DB, Bacteria DB, and PHAST result DB. Pre-calculated genomes for viewing are also available.

Proper citation: PHAge Search Tool (RRID:SCR_005184) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/FLASH/

Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data.

Proper citation: FLASH (RRID:SCR_005531) Copy   

•   Source: SciCrunch Registry