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http://www.ncbi.nlm.nih.gov/clinvar/

Archive of aggregated information about sequence variation and its relationship to human health. Provides reports of relationships among human variations and phenotypes along with supporting evidence. Submissions from clinical testing labs, research labs, locus-specific databases, expert panels and professional societies are welcome. Collects reports of variants found in patient samples, assertions made regarding their clinical significance, information about submitter, and other supporting data. Alleles described in submissions are mapped to reference sequences, and reported according to HGVS standard.

Proper citation: ClinVar (RRID:SCR_006169) Copy   

•   Source: SciCrunch Registry

http://www.vmatch.de/

Software tool for efficiently solving large scale sequence matching tasks.

Proper citation: Vmatch (RRID:SCR_018968) Copy   

•   Source: SciCrunch Registry

https://github.com/oushujun/LTR_FINDER_parallel

Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons.

Proper citation: LTR_FINDER_parallel (RRID:SCR_018969) Copy   

•   Source: SciCrunch Registry

https://github.com/acg-team/tral

Software tool to make annotation of tandem repeats in amino acid and nucleic data simple. Includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs. Used for statistical significance analysis of putative tandem repeats, and filtering of redundant predictions.

Proper citation: TRAL (RRID:SCR_018979) Copy   

•   Source: SciCrunch Registry

https://evcouplings.org/

Web server provides functional and structural information about proteins from their evolutionary record using methods from statistical physics. Computes evolutionary couplings from sequence alignments and predicts 3D structure for your protein of interest. Allows to run former EVcouplings, EVmutation, EVfold and EVcomplex jobs.

Proper citation: Evolutionary Couplings Server (RRID:SCR_018745) Copy   

•   Source: SciCrunch Registry

http://annotree.uwaterloo.ca/

Web tool for visualization of genome annotations across large phylogenetic trees.Used for visualization and exploration of functionally annotated microbial tree of life. Integrates taxonomic, phylogenetic and functional annotation data from bacterial and archaeal genomes.

Proper citation: Annotree (RRID:SCR_018980) Copy   

•   Source: SciCrunch Registry

https://github.com/BackofenLab/StoatyDive

Software tool to evaluate and classify predicted peak profiles to assess binding specificity of protein to its targets. Can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data.

Proper citation: StoatyDive (RRID:SCR_018796) Copy   

•   Source: SciCrunch Registry

https://github.com/Gaius-Augustus/BRAKER

Software tool as pipeline for accurate and automated gene prediction in novel eukaryotic genomes. Automated gene prediction training and gene prediction pipeline.BRAKER1 is eukaryotic genome annotation pipeline. BRAKER2 is extension of BRAKER1 which allows for fully automated training of gene prediction tools GeneMark EX R14, R15, R17, F1 and AUGUSTUS from RNA Seq and/or protein homology information, and that integrates extrinsic evidence from RNA-Seq and protein homology information into prediction.

Proper citation: BRAKER (RRID:SCR_018964) Copy   

•   Source: SciCrunch Registry

http://www.imgt.org/StatClonotype/

Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences.

Proper citation: IMGT/StatClonotype (RRID:SCR_018963) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/seqtk

Software fast and lightweight tool for processing sequences in FASTA or FASTQ format.

Proper citation: Seqtk (RRID:SCR_018927) Copy   

•   Source: SciCrunch Registry

https://github.com/sandmanns/CopyDetective

Software tool for detection threshold aware CNV calling in matched whole exome sequencing data.

Proper citation: CopyDetective (RRID:SCR_018909) Copy   

•   Source: SciCrunch Registry

https://github.com/cochran4/GEMB

Software tool to introduce gene set enrichment for mathematical biology. Measures association between disease of interest and set of genes related to biological pathway. Used for defining gene contributions based on biophysical properties, by leveraging mathematical models of biology to predict effects of genetic perturbations on particular downstream function.

Proper citation: GEMB (RRID:SCR_018904) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi

Web tool for detection of structural and functional domains in protein sequences. Allows computation and download of conserved domain annotation for large sets of protein queries. Allows to view results graphically. Shows domain footprints, alignment details, and conserved features on any individual query sequence.

Proper citation: Batch Web CD-Search Tool (RRID:SCR_018756) Copy   

•   Source: SciCrunch Registry

https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/

Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data.

Proper citation: RiboTaper (RRID:SCR_018880) Copy   

•   Source: SciCrunch Registry

https://github.com/SouthGreenPlatform/metaXplor

Web interfaced application to store, share, explore and manipulate metagenomic data. Interactive viral and microbial metagenomic data manager. Stores large volumes of user defined sample, sequence and assignment information while providing filtering web interface. Offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. Available as set of Docker containers that make it simple to deploy on various infrastructures.

Proper citation: metaXplor (RRID:SCR_019025) Copy   

•   Source: SciCrunch Registry

https://github.com/LCSB-BioCore/GigaSOM.jl

Software tool for huge scale, high performance flow cytometry data clustering and visualization in Julia. High performance clustering and visualization of huge cytometry datasets.

Proper citation: GigaSOM.jl (RRID:SCR_019020) Copy   

•   Source: SciCrunch Registry

http://crdd.osdd.net/raghava/vicmpred/index.html

Software tool as SVM based method for prediction of functional proteins of gram negative bacteria using amino acid patterns and composition. Webserver for functional classification of proteins of bacteria into virulence factors, information molecule, cellular process and metabolism molecule.

Proper citation: VICMpred (RRID:SCR_019039) Copy   

•   Source: SciCrunch Registry

http://pyntacle.css-mendel.it/

Software Python package and command line tool for graphs analysis. Used to search for important components of graphs. Implements and provides ancillary methods for community finding, set operations between graphs, and quick data type conversion tools.

Proper citation: Pyntacle (RRID:SCR_019030) Copy   

•   Source: SciCrunch Registry

https://github.com/auranic/ClinTrajan

Software Python package for analysis of trajectories in clinical datasets.

Proper citation: ClinTrajAn (RRID:SCR_019018) Copy   

•   Source: SciCrunch Registry

http://www.genoscope.cns.fr/gmove

Software tool for genome annotation. Eukaryotic gene prediction tool focused on evidence supported by expressed sequences like transcripts and conserved proteins alignments. Can be used to reannotate genomes, to do comparative gene prediction and improve existing genome annotation. Can predict gene models with canonical and non-canonical splice sites.

Proper citation: Gmove (RRID:SCR_019132) Copy   

•   Source: SciCrunch Registry