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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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VeryFastTree Resource Report Resource Website 1+ mentions |
VeryFastTree (RRID:SCR_023594) | software application, source code, software resource | Software tool for speeding up estimation of phylogenetic trees for large alignments through parallelization and vectorization strategies. | large alignments, phylogenetic tree, phylogenetic tree creation, bio.tools |
is listed by: bio.tools is related to: FastTree |
MICINN ; Xunta de Galicia ; ERDF |
PMID:32573652 DOI:10.1093/bioinformatics/btaa582 |
Free, Available for download, Freely available | biotools:veryfasttree | https://bio.tools/veryfasttree | SCR_023594 | 2026-02-15 09:22:29 | 5 | ||||||
|
FATCAT Resource Report Resource Website 100+ mentions |
FATCAT (RRID:SCR_014631) | web application, software resource | Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | web server, protein, comparison, structure, flexible protein structure, protein structure comparison, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: FATCAT Flexible Structural Neighborhood |
NIGMS GM101457; NIGMS GM63208; NIGMS GM076221; NSF DBI-0349600 |
PMID:14534198 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fatcat | https://bio.tools/fatcat | SCR_014631 | (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists, (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (FATCAT) | 2026-02-15 09:21:06 | 139 | |||||
|
Telescope Resource Report Resource Website 1+ mentions |
Telescope (RRID:SCR_017626) | web application, software resource | Open source web application that tracks progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system. Allows remote scheduling of pre-defined pipelines, as well as re-scheduling queued jobs. Telescope does not assume anything from the remote server, except for SSH connection. The connection is established using SSH key pairs that are stored after encrypted. | Track, progress, remote, server, scheduling, system, on demand, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at Los Angeles; California; USA |
Free, Freely available | biotools:telescope | https://bio.tools/Telescope | SCR_017626 | 2026-02-15 09:22:10 | 2 | ||||||||
|
Vienna RNA Resource Report Resource Website 100+ mentions |
Vienna RNA (RRID:SCR_008550) | data or information resource, database, software resource | This server provides programs, web services, and databases, related to our work on RNA secondary structures. For general information and other offerings from our group see the main TBI web server. With the 1st of May 2009 we updated our servers to the Vienna RNA package version 1.8.2! The Vienna RNA Servers: * RNAfold server predicts minimum free energy structures and base pair probabilities from single RNA or DNA sequences. * RNAalifold server predicts consensus secondary structures from an alignment of several related RNA or DNA sequences. You need to upload an alignment. * RNAinverse server allows you to design RNA sequences for any desired target secondary structure. * RNAcofold server allows you to predict the secondary structure of a dimer. * RNAup server allows you to predict the accessibility of a target region. * LocARNA server generates structural alignments from a set of sequences. In collaboration with the Bioinformatics Group Freiburg. * barriers server allows you to get insights into RNA folding kinetics. * RNAz server will assist you in detecting thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments. * Structure conservation analysis server will assist you in detecting evolutionarily conserved RNA secondary structures in multiple sequence alignments. * RNAstrand server allows you to predict the reading direction of evolutionarily conserved RNA secondary structures. * RNAxs server assists you in siRNA design. * Bcheck predicts rnpB genes Downloads Get the Source code for: * the Vienna RNA Package, our basic RNA secondary structure analysis software. * The ALIDOT package for finding conserved structure motifs (add-on) * The barriers program for analysis of RNA folding landscapes. Databases * Atlas of conserved Viral RNA Structures found by ALIDOT | bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: ANNOgesic has parent organization: University of Vienna; Vienna; Austria |
DOI:10.1186/1748-7188-6-26 | biotools:vienna_rna_package, nif-0000-31411, OMICS_09351 | https://bio.tools/vienna_rna_package https://sources.debian.org/src/vienna-rna/ |
SCR_008550 | Vienna RNA | 2026-02-15 09:19:51 | 404 | |||||||
|
BARS Resource Report Resource Website 10+ mentions |
BARS (RRID:SCR_009123) | BARS | software application, software resource | Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154204, biotools:bars, nlx_154228, SCR_009106 | https://bio.tools/bars | SCR_009123 | Bayesian Adaptive Regression Splines | 2026-02-15 09:19:57 | 39 | ||||||
|
Sybil Resource Report Resource Website 10+ mentions |
Sybil (RRID:SCR_005593) | Sybil | data or information resource, database, software resource | A web-based software package for comparative genomics. | comparative genomics, genome, synteny, protein cluster, protein, gene, genomic region, synteny gradient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22121156 | OMICS_00945, biotools:sybil | https://bio.tools/sybil | SCR_005593 | Sybil: Web-based software for comparative genomics | 2026-02-15 09:19:00 | 37 | ||||||
|
Database of Secondary Structure Assignments Resource Report Resource Website 50+ mentions |
Database of Secondary Structure Assignments (RRID:SCR_002725) | DSSP | data or information resource, database, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB) and the program that calculates DSSP entries from PDB entries. DSSP is distributed on a basis of trust and instructions are available on the site. * Precompiled executables are also available for Linux and Windows. (The Windows .exe file was compiled under Linux using Mingw32, has never seen a Windows environment and should thus be virus-free. Download the source if you want to be 100% sure.) Under Windows the DSSP output does not make it to the console, so redirect it to a file instead: dsspcmbi source.pdb destination.dssp > messages.txt * Several changes have been made to the DSSP program to solve problems with recent PDB files. These are documented in the source code. * FTP access to the DSSP files resides at the CMBI: ftp.cmbi.kun.nl/pub/molbio/data/dssp or ftp://ftp.ebi.ac.uk/pub/databases/dssp/. If you have problems downloading the DSSP files, it is likely that your FTP program is not able to handle tens of thousands of files in one directory. In this case, install a proper FTP program, for example NCFTP. However, it is recommended that you download DSSP files with the rsync command. | amino acid sequence, hydrogen bonding, protein conformation, proteins, gold standard, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Radboud University; Nijmegen; The Netherlands |
PMID:6667333 PMID:21071423 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-23901, biotools:dssp, OMICS_06247 | http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+DSSP https://bio.tools/dssp https://sources.debian.org/src/dssp/ |
http://www.sander.ebi.ac.uk/dssp/ | SCR_002725 | 2026-02-15 09:18:23 | 59 | |||||
|
Segway - a way to segment the genome Resource Report Resource Website 1+ mentions |
Segway - a way to segment the genome (RRID:SCR_004206) | source code, software resource | The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. The method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. Segway uses the Graphical Models Toolkit (GMTK) for efficient DBN inference. The software has extensive documentation and was designed from the outset with external users in mind. | genome annotation, source code, bayesian network model, bayesian, chip seq, dbn, bio.tools |
is used by: ENCODE is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA has parent organization: University of Toronto; Ontario; Canada |
PMID:22426492 | Free | nlx_22911, biotools:segway | https://www.pmgenomics.ca/hoffmanlab/proj/segway/ https://bitbucket.org/hoffmanlab/segway/ https://bio.tools/segway |
http://noble.gs.washington.edu/proj/segway/ | SCR_004206 | Segway | 2026-02-15 09:18:39 | 8 | |||||
|
CUDASW++ Resource Report Resource Website 1+ mentions |
CUDASW++ (RRID:SCR_008862) | CUDASW++ | source code, software resource | CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher | smith-waterman, bioinformatics, protein, protein database, sequence, simt, simd, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Nanyang Technological University; Singapore; Singapore |
PMID:19416548 PMID:20370891 |
Open-source | nlx_149212, biotools:cudasw | https://bio.tools/cudasw | SCR_008862 | CUDASW++ (Smith Waterman) | 2026-02-15 09:19:58 | 5 | |||||
|
PEDIGREEQUERY Resource Report Resource Website 1+ mentions |
PEDIGREEQUERY (RRID:SCR_009041) | PEDIGREEQUERY | software application, software resource | Software application that allows drawing pedigrees with a difficult structure, those containing consanguinity loops, and those individuals with multiple mates or several related families (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154007, biotools:pedcut | https://bio.tools/pedcut | SCR_009041 | 2026-02-15 09:20:02 | 1 | ||||||||
|
FASTSLINK Resource Report Resource Website 10+ mentions |
FASTSLINK (RRID:SCR_008664) | FASTSLINK | software application, software resource | Software application that is a faster version of SLINK (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: SLINK is related to: SUP |
nlx_154312, biotools:snpcaller | https://bio.tools/snpcaller | SCR_008664 | faster SLINK | 2026-02-15 09:19:52 | 12 | |||||||
|
PEDPEEL Resource Report Resource Website |
PEDPEEL (RRID:SCR_008436) | PEDPEEL | software application, software resource | Software program that prepares pedigree data for calculation of Elston-Stewarts'' likelihood function. It finds an optimal way to peel a pedigree and returns text file containing 7 description arrays (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154524, biotools:pedpeel | https://bio.tools/pedpeel | SCR_008436 | 2026-02-15 09:19:49 | 0 | ||||||||
|
ADMIXMAP Resource Report Resource Website 10+ mentions |
ADMIXMAP (RRID:SCR_009035) | ADMIXMAP | software application, software resource | General-purpose program for modelling admixture, using marker genotypes and trait data on a sample of individuals from an admixed population (such as African-Americans), where the markers have been chosen to have extreme differentials in allele frequencies between two or more of the ancestral populations between which admixture has occurred. The main difference between ADMIXMAP and classical programs for estimation of admixture such as ADMIX is that ADMIXMAP is based on a multilevel model for the distribution of individual admixture in the population and the stochastic variation of ancestry on hybrid chromosomes. This makes it possible to model the associations of ancestry between linked marker loci, and the association of a trait with individual admixture or with ancestry at a linked marker locus. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, linux, ms-windows, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_153999, biotools:admixmap | https://bio.tools/admixmap | SCR_009035 | Admixture mapping | 2026-02-15 09:19:37 | 19 | |||||||
|
MOSCPHASER Resource Report Resource Website |
MOSCPHASER (RRID:SCR_009092) | MOSCPHASER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software application for inferring haplotypes composed of both CNV alleles and SNP alleles. | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools |
PMID:18492685 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154109, biotools:mocsphaser | https://bio.tools/mocsphaser | http://emu.src.riken.jp/MOCSphase/MOSCphaser.zip | SCR_009092 | Mixture Of Cnv-Snp PHASER | 2026-02-15 09:19:57 | 0 | ||||
|
GLUE Resource Report Resource Website 10+ mentions |
GLUE (RRID:SCR_009211) | GLUE | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. A web interface to several commonly used statistical genetics programs, including Linkage, Genehunter, Merlin, Unphased, and Transmit. It simplifies their use through graphical selection of program options, automation of multiple analyses, and viewing of graphical output. GLUE is available to HGMP account holders; registration is free to all academic users., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, perl, any web browser, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154360, biotools:GLUE | https://bio.tools/GLUE | http://portal.litbio.org/Registered/Webapp/glue/ | SCR_009211 | Genetic Linkage User Environment | 2026-02-15 09:20:07 | 46 | |||||
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TWOLOC Resource Report Resource Website |
TWOLOC (RRID:SCR_009230) | TWOLOC | software application, software resource | Software package for analyzing two-locus susceptibility gene models in affected sib-pair data (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran77, pascal, awk, unix, (saloris/dec unix/irix/..), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154387, biotools:twoloc | https://bio.tools/twoloc | SCR_009230 | 2026-02-15 09:19:59 | 0 | ||||||||
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GENERECON Resource Report Resource Website 1+ mentions |
GENERECON (RRID:SCR_009195) | GENERECON | software application, software resource | Software application for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, linux, macos, ms-windows, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154338, biotools:generecon | https://bio.tools/generecon | SCR_009195 | 2026-02-15 09:20:06 | 1 | ||||||||
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HTR Resource Report Resource Website 1+ mentions |
HTR (RRID:SCR_009241) | HTR | software application, software resource | Software application for haplotype association mapping using unrelated individuals; fixed and sliding window analysis; overall tests and tests for individual haplotype effects (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, bash shell, ms-windows, unix, solaris, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154402, biotools:htr | https://bio.tools/htr | SCR_009241 | Haplotype Trend Regression | 2026-02-15 09:20:06 | 1 | |||||||
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MULTIDISEQ Resource Report Resource Website |
MULTIDISEQ (RRID:SCR_009304) | MULTIDISEQ | software application, software resource | A multipoint linkage analysis software which allows Marker-Marker LD (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154494, biotools:multidiseq | https://bio.tools/multidiseq | SCR_009304 | 2026-02-15 09:20:06 | 0 | ||||||||
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MPDA Resource Report Resource Website 10+ mentions |
MPDA (RRID:SCR_009303) | MPDA | software application, software resource | A tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. MPDA was developed under the software platform, MATLABR, and provided user-friendly interfaces adapted to Windows systems (Windows 98, Windows 2000 and Windows XP). or users without installing software MATLABR, we also developed stand-alone executables generated via the MATLABR compiler. MPDA provides four major functions: (1) Whole-genome DNA amplification/hybridization analysis, (2) Allele frequency estimation, (3) Association mapping, (4) Allelic imbalance detection. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data. (entry from Genetic Analysis Software) | gene, genetic, genomic, matlabr, ms-windows, (windows98/2000/xp), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:mpda, nlx_154492 | https://bio.tools/mpda | SCR_009303 | Microarray Pooled DNA Analyser | 2026-02-15 09:20:10 | 12 |
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