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https://github.com/qmarcou/IGoR/

C++ software designed to infer V(D)J recombination related processes from sequencing data.

Proper citation: IGoR (RRID:SCR_024053) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/paulklemm_PHD/proteinortho

Software tool to detect orthologous genes within different species. Stand-alone tool for large datasets for orthology analysis.

Proper citation: Proteinortho (RRID:SCR_024177) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/genomicepidemiology/kmerresistance/src/master/

Software tool to correlate mapped genes with the predicted species of WGS samples, where this allows for identification of genes in samples which have been poorly sequenced or high accuracy predictions for samples with contamination. KmerResistance has one dependency, namely KMA to perform the mapping, which is also freely available.

Proper citation: KmerResistance (RRID:SCR_024058) Copy   

•   Source: SciCrunch Registry

http://proda.stanford.edu/

Software for multiple alignment of protein sequences with repeated and shuffled elements.Used for automated detection and alignment of homologous regions in collections of proteins with arbitrary domain architectures.

Proper citation: ProDA (RRID:SCR_024171) Copy   

•   Source: SciCrunch Registry

https://github.com/klebgenomics/Kleborate

Software tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for MLST sequence type, species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.), ICEKp associated virulence loci (yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)), virulence plasmid associated loci (salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)), antimicrobial resistance determinants (acquired genes, SNPs, gene truncations and intrinsic ?-lactamases), and K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive.

Proper citation: Kleborate (RRID:SCR_024051) Copy   

•   Source: SciCrunch Registry

http://www.swisstargetprediction.ch/

Web tool to estimate the most probable macromolecular targets of small molecule, assumed as bioactive. Prediction is founded on combination of 2D and 3D similarity with library of known actives on proteins from three different species.

Proper citation: SwissTargetPrediction (RRID:SCR_023756) Copy   

•   Source: SciCrunch Registry

https://ukoethe.github.io/vigra/

Software image processing and analysis library that puts its main emphasis on customizable algorithms and data structures. VIGRA is especially strong for multi-dimensional images. By using template techniques similar to those in the C++ Standard Template Library, you can easily adapt any VIGRA component to the needs of your application, without thereby giving up execution speed. As of version 1.7.1, VIGRA also provides extensive Python bindings on the basis of the popular numpy framework.

Proper citation: VIGRA (RRID:SCR_024100) Copy   

•   Source: SciCrunch Registry

https://github.com/biocore/pynast

Software tool for aligning sequences to template alignment.

Proper citation: pynast (RRID:SCR_024189) Copy   

•   Source: SciCrunch Registry

https://www.imsc.res.in/~rsidd/sigma/

Software alignment program with new algorithm and scoring scheme designed specifically for non-coding DNA sequence. This problem is now growing in importance with the increasing number of fully-sequenced species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms (such as PhyloGibbs) for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step.

Proper citation: sigma-align (RRID:SCR_024337) Copy   

•   Source: SciCrunch Registry

https://github.com/ArtRand/signalAlign

Software tool to align ionic current from MinION to reference sequence using trainable hidden Markov model. HMM-HDP models for MinION signal alignments,

Proper citation: signalalign (RRID:SCR_024339) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.org/patristic/

Software Java program for calculating patristic distances and graphically comparing the components of genetic change.

Proper citation: Patristic (RRID:SCR_024154) Copy   

•   Source: SciCrunch Registry

https://docs.igdiscover.se/en/stable/

Software to analyze antibody repertoires and discover new V genes from high-throughput sequencing reads.Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: IgDiscover (RRID:SCR_024037) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/alkesgroup/BOLT-LMM/

Software statistical tool for identifying genetic associations. Used for genome wide association studies in large cohorts.

Proper citation: BOLT-LMM (RRID:SCR_023978) Copy   

•   Source: SciCrunch Registry

https://quint-workflow.readthedocs.io/en/latest/QUINTintro.html

Software workflow includes suite of various software to form analysis pipeline of atlas-based quantifuication of labbeled features in histological images from mouse or rat brain. This workflow also suggests and explains with instructional videos the way these software work together. Used for quantification and spatial analysis of labelling in series of rodent brain section images based on available 3D reference atlases.

Proper citation: QUINT (RRID:SCR_023856) Copy   

•   Source: SciCrunch Registry

https://github.com/brainglobe/brainreg-segment

Software tool for manual segmentation of regions/objects within the brain. Brainreg-segment will only work if the user registers their data with brainreg first. Used for segmentation of 3D shapes in common anatomical space.

Proper citation: Brainreg-segment (RRID:SCR_023853) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/iva

Software tool as de novo assembler designed to assemble virus genomes that have no repeat sequences,using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.

Proper citation: IVA (RRID:SCR_024044) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfo-ut/PlasmidSeeker

Software tool as k-mer based program for identification of known plasmids from whole genome sequencing reads. Used for identification of known plasmids from bacterial whole genome sequencing reads.

Proper citation: PlasmidSeeker (RRID:SCR_024167) Copy   

•   Source: SciCrunch Registry

http://contra.stanford.edu/contrafold/

Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction.

Proper citation: CONTRAfold (RRID:SCR_023994) Copy   

•   Source: SciCrunch Registry

https://github.com/omnideconv/immunedeconv

Software R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data.

Proper citation: Immunedeconv (RRID:SCR_023869) Copy   

•   Source: SciCrunch Registry

http://codonw.sourceforge.net

Software tool designed to simplify Multivariate analysis (correspondence analysis) of codon and amino acid usage. It also calculates standard indices of codon usage.

Proper citation: CodonW (RRID:SCR_023989) Copy   

•   Source: SciCrunch Registry