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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Pecan Resource Report Resource Website 50+ mentions |
Pecan (RRID:SCR_001909) | software resource | A Java consistency based multiple sequence alignment software program. | java, sequence, alignment, consistency, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Santa Cruz; California; USA |
PMID:18849524 | Free, Available for download, Freely available | OMICS_03739, biotools:pecan | http://hgwdev.cse.ucsc.edu/~benedict/code/Pecan.html, https://bio.tools/pecan | SCR_001909 | 2026-08-01 12:02:06 | 50 | |||||||
|
TCW Resource Report Resource Website 1+ mentions |
TCW (RRID:SCR_001875) | TCW | software resource | Software package for assembling, annotating, querying, and comparing transcript and expression level data that consists of two parts: * singleTCW (sTCW): Single transcript sets or assemblies; annotation; differential expression (EdgeR, DEGSeq, DESeq, GoSeq) * multiTCW (mTCW): Comparison of multiple transcript sets; ortholog grouping (e.g., OrthoMCL) It has been tested on Linux and uses Java, mySQL and optionally R. | transcript, assembly annotation, differential expression, transcript set, ortholog, expression, linux, java, mysql, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Arizona; Arizona; USA |
NSF IOS-1044821 | PMID:23874959 | Free, Available for download, Freely available | OMICS_01940, biotools:tCW | https://bio.tools/TCW | SCR_001875 | Transcriptome Computational Workbench, TCW: Transcriptome Computational Workbench | 2026-08-01 12:01:53 | 2 | ||||
|
TEMP Resource Report Resource Website 100+ mentions |
TEMP (RRID:SCR_001788) | software resource | Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Massachusetts Medical School; Massachusetts; USA |
PMID:24753423 | Free, Available for download, Freely available | OMICS_03821, biotools:temp | https://bio.tools/temp | SCR_001788 | 2026-08-01 12:02:03 | 211 | |||||||
|
AffyPipe Resource Report Resource Website 1+ mentions |
AffyPipe (RRID:SCR_002032) | software resource | An open-source software pipeline for Affymetrix Axiom genotyping workflow. | affymetrix, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Italian Ministry of Education University and Research 505/Ric; project GenHome ; European Union FP7 project Gene2Farm 289592 |
PMID:25028724 | Free, Available for download, Freely available | biotools:affypipe, OMICS_05203 | https://bio.tools/affypipe | SCR_002032 | AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow | 2026-08-01 12:01:57 | 5 | |||||
|
CanSNPer Resource Report Resource Website 10+ mentions |
CanSNPer (RRID:SCR_001980) | software resource | Software that is a hierarchical genotype classifier of clonal pathogens. | python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24574113 | Free, Available for download, Freely available | biotools:cansnper, OMICS_03706 | https://bio.tools/cansnper | SCR_001980 | 2026-08-01 12:01:40 | 18 | |||||||
|
Ray Resource Report Resource Website 1+ mentions |
Ray (RRID:SCR_001916) | Ray | software resource | Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2. | mpi, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20958248 DOI:10.1089/cmb.2009.0238 |
Free, Available for download, Freely available | OMICS_00027, biotools:ray | https://bio.tools/ray, https://sources.debian.org/src/ray/ | SCR_001916 | Ray - a de novo assembler using MPI 2.2, Ray - Parallel genome assemblies for parallel DNA sequencing | 2026-08-01 12:01:55 | 1 | |||||
|
Cake Resource Report Resource Website 10+ mentions |
Cake (RRID:SCR_002133) | software resource | A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. | standalone software, unix/linux, mac os x, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23803469 | Free, Available for download, Freely available | OMICS_03613, biotools:cake | https://bio.tools/cake | SCR_002133 | 2026-08-01 12:01:42 | 11 | |||||||
|
SBARS Resource Report Resource Website |
SBARS (RRID:SCR_002371) | software resource | Bioinformatics tool for searching different types of long repeats in sequences comparable by size with chromosomes. | linux, windows, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24532721 | OMICS_03432, biotools:sbars | https://bio.tools/sbars | SCR_002371 | S.B.A.R.S, S.B.A.R.S., S.B.A.R.S - Spectral-Based Approach for Repeats Search, Spectral-Based Approach for Repeats Search | 2026-08-01 12:02:05 | 0 | |||||||
|
CAMERA - Collection of annotation related methods for mass spectrometry data Resource Report Resource Website 1+ mentions |
CAMERA - Collection of annotation related methods for mass spectrometry data (RRID:SCR_002466) | CAMERA | software resource | A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data. | standalone software, mac os x, unix/linux, windows, r, spectra, extraction, annotation, liquid chromatography, mass spectrometry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:22111785 | Free, Available for download, Freely available | biotools:camera, OMICS_03366 | https://bio.tools/camera | SCR_002466 | CAMERA - Collection of annotation related methods for mass spectrometry data | 2026-08-01 12:02:10 | 4 | |||||
|
PolyPhred Resource Report Resource Website 100+ mentions |
PolyPhred (RRID:SCR_002337) | PolyPhred | software resource | Software program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. Its functions are integrated with the use of three other programs: Phred (Brent Ewing and Phil Green), Phrap (Phil Green), and Consed (David Gordon and Phil Green). PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool. | windows, sequence, nucleotide substitution, heterozygote, polymorphic, genotype, single nucleotide polymorphism, fluorescence, single nucleotide substitution, polymorphism, insertion, deletion, indel, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:17115056 PMID:16493422 PMID:9207020 |
Free for academic use, Commercial use requires a license | biotools:polyphred, OMICS_01815 | https://bio.tools/polyphred | SCR_002337 | 2026-08-01 12:01:46 | 123 | ||||||
|
Iterative Signature Algorithm Resource Report Resource Website |
Iterative Signature Algorithm (RRID:SCR_002327) | isa2, ISA | software resource | A biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix. | standalone software, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:12689096 | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 | biotools:isa, OMICS_03487 | https://bio.tools/isa | SCR_002327 | isa2: The Iterative Signature Algorithm | 2026-08-01 12:02:09 | 0 | |||||
|
NCBI Structure: Cn3D Resource Report Resource Website 100+ mentions |
NCBI Structure: Cn3D (RRID:SCR_004861) | d visualization software | Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI''s Entrez retrieval service. Cn3D runs on Windows, Macintosh, and Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features. Cn3D is a tool for visualization of three-dimensional structures with emphasis on interactive examination of sequence-structure relationships and superposition of geometrically similar structures. Can be used to display MMDB structures, superpositions of VAST related structures, and conserved core motifs identified in conserved domains. | gold standard, bio.tools |
is listed by: bio.tools is related to: NCBI Structure has parent organization: NCBI |
PMID:10838572 | biotools:cn3d, nlx_84208 | https://bio.tools/cn3d | SCR_004861 | Cn3D | 2026-08-01 12:02:45 | 130 | |||||||
|
MetaPhyler Resource Report Resource Website 10+ mentions |
MetaPhyler (RRID:SCR_004848) | software resource | A taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. The classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. The reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database. | metagenome, classification, sequence, taxonomy, genome, microbiome, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: University of Maryland; Maryland; USA |
PMID:21989143 | Acknowledgement requested, Available for download | OMICS_01455, biotools:metaphyler | https://bio.tools/metaphyler | SCR_004848 | MetaPhyler - Estimating Bacterial Composition from Metagenomic Sequences | 2026-08-01 12:02:45 | 11 | ||||||
|
hyfi: software suite for binding site search Resource Report Resource Website |
hyfi: software suite for binding site search (RRID:SCR_004884) | software resource | This collection of software is designed to rapidly identify identifies primer and microarray probe binding sites for a query sequence in genomic DNA. This software suite has four main programs:1. A program for indexing a sequence file to speed up the binding site search. 2. A program for retrieving the binding sites of a query sequence. 3. A program for identifying sites where PCR primers could co-operate to exponentially amplify a sequence 4. A program for analyzing a set of binding sites to tailor the search for different reaction conditions. This software is implemented in C. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:16873493 | nlx_85657, biotools:hyfi | https://bio.tools/hyfi | SCR_004884 | Hyfi | 2026-08-01 12:02:46 | 0 | |||||||
|
USeq Resource Report Resource Website 100+ mentions |
USeq (RRID:SCR_004753) | USeq | software resource | A collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_00499, biotools:useq | https://bio.tools/useq | SCR_004753 | 2026-08-01 12:02:45 | 124 | ||||||||
|
miRNAKey Resource Report Resource Website 1+ mentions |
miRNAKey (RRID:SCR_004813) | miRNAKey | software resource | A software pipeline for the analysis of microRNA Deep Sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20801911 | OMICS_00364, biotools:mirnakey | https://bio.tools/mirnakey | SCR_004813 | 2026-08-01 12:02:45 | 6 | |||||||
|
SVMerge Resource Report Resource Website 10+ mentions |
SVMerge (RRID:SCR_004777) | SVMerge | software resource | Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available. | structural variant, breakpoint, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:21194472 | biotools:svmerge, OMICS_00325 | https://bio.tools/svmerge | SCR_004777 | SVMerge - Enhanced structural variant and breakpoint detection | 2026-08-01 12:02:40 | 19 | ||||||
|
SVseq Resource Report Resource Website 1+ mentions |
SVseq (RRID:SCR_004804) | SVseq | software resource | Software for accurate and efficient calling of structural variations with low-coverage sequence data. Version 2 uses the BAM files of paired Illumina reads with soft-clip signature as input. It calls both deletions and insertions. | structural variant, deletion, insertion, breakpoint, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Connecticut; Connecticut; USA |
PMID:22537045 | OMICS_00327, biotools:svseq | https://bio.tools/svseq | SCR_004804 | SVseq2, SVseq1 | 2026-08-01 12:02:46 | 3 | ||||||
|
Minia Resource Report Resource Website 50+ mentions |
Minia (RRID:SCR_004986) | Minia | software resource | A short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1748-7188-8-22 | biotools:minia, OMICS_00022 | https://bio.tools/minia, https://sources.debian.org/src/minia/ | SCR_004986 | 2026-08-01 12:02:43 | 62 | |||||||
|
MIP Scaffolder Resource Report Resource Website 1+ mentions |
MIP Scaffolder (RRID:SCR_005072) | MIP Scaffolder | software resource | A software program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Helsinki; Helsinki; Finland |
OMICS_00044, biotools:mip_scaffolder | https://bio.tools/mip_scaffolder | SCR_005072 | 2026-08-01 12:02:53 | 1 |
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