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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SMILE Resource Report Resource Website 1+ mentions |
SMILE (RRID:SCR_024119) | software application, software resource | Software tool that infers motifs in set of sequences to infer exceptionnal sites as binding sites in DNA sequences. 1.4 version allows to infer motifs written on any alphabet in any kind of sequences. Allows to deal with motifs associated by some distance constraints. Used to group under unique model different occurrences composed of several boxes separated by spacers of different lengths. | infers motifs in set of sequences, binding sites in DNA sequences, distance constraints, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_20188 | https://sources.debian.org/src/mlv-smile/ | SCR_024119 | mlv-smile | 2026-02-15 09:23:34 | 1 | |||||||
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samclip Resource Report Resource Website 1+ mentions |
samclip (RRID:SCR_024330) | software application, software resource | Software tool to filter SAM file for soft and hard clipped alignments | filter SAM file, soft and hard clipped alignments, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/samclip/ | SCR_024330 | 2026-02-15 09:23:40 | 2 | |||||||||
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seqwish Resource Report Resource Website |
seqwish (RRID:SCR_024332) | software application, software resource | Software tool for alignment to variation graph inducer. | alignment, variation graph inducer, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/seqwish/ | SCR_024332 | 2026-02-15 09:23:29 | 0 | |||||||||
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sigviewer Resource Report Resource Website |
sigviewer (RRID:SCR_024340) | software application, software resource | Software viewing application for biosignals such as EEG or MEG time series. In addition to viewing raw data, SigViewer can also create, edit, and display event information such as annotations or artifact selections. | viewing application for biosignals, EEG, MEG, time series, viewing raw data, create event information, edit event information, display event information, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/sigviewer/ | SCR_024340 | 2026-02-15 09:23:29 | 0 | |||||||||
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sitplus Resource Report Resource Website |
sitplus (RRID:SCR_024344) | software application, software resource | Software framework to provide ludic-therapeutic activities for people with disabilities.Offers new forms of interaction based on computer vision, voice and other peripherals to produce result in form of image and sound. Used for continuous and remote interaction, attainable to majority of people with cognitive, sensory and physical disabilities. | interaction based on computer vision, voice, produce result in form of image and sound, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/sitplus/ | SCR_024344 | SITPLUS | 2026-02-15 09:23:29 | 0 | ||||||||
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tacg Resource Report Resource Website |
tacg (RRID:SCR_024374) | software application, software resource | Software tool as command line program that performs many of the common routines in pattern matching in biological strings. It was originally designed for restriction enzyme analysis and while that still forms core of the program, it has been expanded to fill more roles, sort of 'grep' for DNA. | pattern matching in biological strings, restriction enzyme analysis, | is listed by: Debian | PMID:11882250 | Free, Available for download, Freely available, | https://sources.debian.org/src/tacg/ | SCR_024374 | 2026-02-15 09:23:30 | 0 | ||||||||
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VelvetOptimiser Resource Report Resource Website 50+ mentions |
VelvetOptimiser (RRID:SCR_024376) | software application, software resource | Software tool to run as wrapper script for Velvet assembler and to assist with optimising the assembly.Used to search supplied hash value range for optimum, estimates expected coverage and then searches for optimum coverage cutoff. Estimates insert lengths for paired end libraries. Can optimise assemblies by default optimisation condition or by user supplied one. It outputs the results to subdirectory and records all its operations in logfile. | wrapper script, Velvet assembler, optimising assembly, optimum search, search supplied hash value range, optimum coverage cutoff, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_14601 | https://sources.debian.org/src/velvetoptimiser/ https://sources.debian.org/src/vsearch/ | SCR_024376 | velvetoptimiser, perl-velvetoptimiser | 2026-02-15 09:23:42 | 55 | |||||||
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VisIt Resource Report Resource Website |
VisIt (RRID:SCR_024370) | software application, software resource | Open source software interactive, scalable, visualization, animation and analysis tool. Used to generate visualizations, animate them through time, manipulate them with variety of operators and mathematical expressions, and save resulting images and animations for presentations. | generate visualizations, animation, analysis, save resulting images and animations for presentations, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/visit/ | SCR_024370 | visit | 2026-02-15 09:23:30 | 0 | ||||||||
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sprai Resource Report Resource Website |
sprai (RRID:SCR_024353) | software application, software resource | Software tool to correct sequencing errors in single pass reads for de novo assembly. | correct sequencing errors, single pass reads, de novo assembly, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_21293 | https://sources.debian.org/src/sprai/ | SCR_024353 | single pass read accuracy improver | 2026-02-15 09:23:27 | 0 | |||||||
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streamlit Resource Report Resource Website 1+ mentions |
streamlit (RRID:SCR_024354) | software application, software resource | Software tool to turn data scripts into shareable web apps in minutes. Faster way to build and share data apps. | turn data scripts into shareable web apps, build and share data apps, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/streamlit/ | SCR_024354 | 2026-02-15 09:23:41 | 6 | |||||||||
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sweed Resource Report Resource Website 1+ mentions |
sweed (RRID:SCR_024357) | software application, software resource | Software tool for likelihood based detection of selective sweeps in thousands of genomes. Software parallel and checkpointable tool that implements composite likelihood ratio test for detecting selective sweeps. | likelihood based detection of selective sweeps, parallel and checkpointable tool, composite likelihood ratio test, detecting selective sweeps, genomes, | is listed by: Debian | PMID:23777627 | Free, Available for download, Freely available, | OMICS_08598 | https://sources.debian.org/src/sweed/ | SCR_024357 | 2026-02-15 09:23:27 | 4 | |||||||
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snpomatic Resource Report Resource Website |
snpomatic (RRID:SCR_024348) | software application, software resource | Short read mapping software. Read mapping tool offering variety of analytical output functions, with emphasis on genotyping, | Short read mapping, analytical output functions, genotyping, | is listed by: Debian | PMID:19574284 | Free, Available for download, Freely available, | OMICS_15114 | https://sources.debian.org/src/snpomatic/ | SCR_024348 | SNP-o-matic | 2026-02-15 09:23:29 | 0 | ||||||
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Workrave Resource Report Resource Website |
Workrave (RRID:SCR_024364) | software application, software resource | Software tool to assist in recovery and prevention of Repetitive Strain Injury. Monitors keyboard and mouse usage and using this information, it frequently alerts you to take microbreaks, rest breaks and restricts you to your daily computer usage. | recovery and prevention of Repetitive Strain Injury, monitor keyboard and mouse usage, microbreaks, rest breaks, daily computer usage restriction, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/workrave/ | SCR_024364 | workrave | 2026-02-15 09:22:41 | 0 | ||||||||
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XMedCon Resource Report Resource Website 1+ mentions |
XMedCon (RRID:SCR_024366) | software application, software resource | Open source software toolkit for medical image conversion. | medical image conversion, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/xmedcon/ | SCR_024366 | xmedcon | 2026-02-15 09:23:30 | 1 | ||||||||
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VMD Resource Report Resource Website 10+ mentions |
VMD (RRID:SCR_024368) | software application, software resource | Software tool as molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. | molecular visualization, displaying, animating, analyzing, large biomolecular systems, . | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/vmd/ | SCR_024368 | vmd | 2026-02-15 09:23:41 | 33 | ||||||||
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ALCHEMY Resource Report Resource Website 1+ mentions |
ALCHEMY (RRID:SCR_005761) | ALCHEMY | source code, software resource | ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed. | diploid, genotype, snp, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Cornell University; New York; USA |
NSF 0606461 | PMID:20926420 | GNU General Public License | biotools:alchemy, nlx_149227 | https://bio.tools/alchemy | SCR_005761 | ALCHEMY - An automated population genetic model driven SNP genotype calling method | 2026-02-15 09:19:11 | 5 | ||||
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BamView Resource Report Resource Website 10+ mentions |
BamView (RRID:SCR_004207) | BamView | source code, software resource | A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub. | bam, next-generation sequencing, java, snp calling, structural annotation, macosx, unix, windows, visualize, analyze, sequence read, reference sequence, single nucleotide polymorphism, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:22253280 PMID:20071372 |
GNU General Public License | biotools:bamview, OMICS_00878, nlx_22933 | https://bio.tools/bamview | SCR_004207 | 2026-02-15 09:18:42 | 21 | ||||||
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Genomedata Resource Report Resource Website |
Genomedata (RRID:SCR_004544) | Genomedata | source code, software resource | A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems. | genome, data, format, linux, mac, functional genomics, function, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:20435580 | GNU General Public License | nlx_53677, biotools:genomedata, OMICS_02148 | https://bio.tools/genomedata | SCR_004544 | 2026-02-15 09:18:45 | 0 | ||||||
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RNAplex Resource Report Resource Website 10+ mentions |
RNAplex (RRID:SCR_002763) | RNAplex | source code, software resource | Software tool to rapidly search for short interactions between two long RNAs. | interaction, rna, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Leipzig; Saxony; Germany |
PMID:21593134 PMID:18434344 |
Free, Freely available, Available for download | rid_000107, biotools:rnaplex | https://bio.tools/rnaplex | SCR_002763 | 2026-02-15 09:18:22 | 37 | ||||||
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TomoMiner Resource Report Resource Website 1+ mentions |
TomoMiner (RRID:SCR_015045) | source code, software resource | Software platform for large-scale cryo electron subtomogram classification, alignment, and averaging. | analysis platform, cryo electron subtomogram, subtomogram classification, subtomogram alignment, subtomogram averaging, subtomogram analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Southern California; Los Angeles; USA requires: Python Programming Language requires: NumPy requires: SciPy requires: LAPACK linear algebra library requires: Cython C-Extensions for Python |
Available for download | biotools:tomominer | https://bio.tools/tomominer | SCR_015045 | 2026-02-15 09:21:05 | 3 |
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