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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SNP HITLINK Resource Report Resource Website |
SNP HITLINK (RRID:SCR_013340) | SNP HITLINK | software resource, software application | Software program providing a useful pipeline to directly connect SNP data and linkage analysis program. SNP HiTLink currently supports the data from SNP chips provided by Affymetrix (Mapping 100k/500k array set, Genome-Wide Human SNP array 5.0/6.0) and Illumina (recently supported), carrying out typical linkage analysis programs of MLINK (FASTLINK/ LINKAGE package), Superlink, Merlin and Allegro. (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_154644, biotools:snp_hitlink | https://bio.tools/snp_hitlink | SCR_013340 | SNP HIgh-Throughput LINKage analysis system | 2026-07-30 09:28:55 | 0 | |||||||
|
THESIAS Resource Report Resource Website 50+ mentions |
THESIAS (RRID:SCR_013449) | THESIAS | software resource, software application | Software program that performs haplotype-based association analysis in unrelated individuals. This program is based on a maximum likelihood model described in Tregouet et al. 2002 and is linked to the stochastic EM (SEM) algorithm. THESIAS allows the simultaneous estimation of haplotype frequencies and of their associated effects on the phenotype of interest. In its current version, both quantitative and qualitative phenotypes can be studied. Covariate-adjusted haplotype effects as well as haplotype x covariate interactions can be investigated. (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btm058 | nlx_154102, OMICS_19747, biotools:tHESIAS | https://bio.tools/THESIAS, https://sources.debian.org/src/thesias/ | http://ecgene.net/genecanvas/downloads.php?cat_id=1 | SCR_013449 | Testing Haplotype EffectS In Association Studies | 2026-07-30 09:29:01 | 51 | |||||
|
PhyML Resource Report Resource Website 5000+ mentions |
PhyML (RRID:SCR_014629) | software resource, web application, source code | Web phylogeny server based on the maximum-likelihood principle. | phylogenic software, phylogeny, maximum likelihood, web server, bio.tools |
is used by: ProtTest is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: PAML |
DOI:10.1093/molbev/msq060 | Public server, Source code is available on request | biotools:phyml, OMICS_04241 | https://bio.tools/phyml, https://sources.debian.org/src/phyml/ | SCR_014629 | 2026-07-30 09:29:21 | 7740 | |||||||
|
ABACAS Resource Report Resource Website 100+ mentions |
ABACAS (RRID:SCR_015852) | ABACAS | software resource, software application | Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account. | contiguation, primer, shotgun assembled contig, reference sequence, assembled sequence |
is listed by: Debian is listed by: OMICtools |
European Union LSHP-LT-2004-503578; Wellcome Trust Sanger Institute |
Free, Available for download | OMICS_06933 | https://sourceforge.net/projects/abacas/files/, https://sources.debian.org/src/abacas/ | SCR_015852 | ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences, Algorithm Based Automatic Contiguation of Assembled Sequences (ABACAS), Algorithm Based Automatic Contiguation of Assembled Sequences | 2026-07-30 09:29:57 | 174 | |||||
|
eXpression2Kinases Resource Report Resource Website 1+ mentions |
eXpression2Kinases (RRID:SCR_016307) | X2K | software resource, software application | Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures. | inferred, network, transcription, factor, protein, kinase, regulate, expression, gene, analysis, combine, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS P50 GM071558; NIDDK R01 DK088541; NLM RC2 LM010994; NIDDK P01 DK056492; NIDDK RC4DK090860; NCRR KL2 RR029885 |
PMID:22080467 | Open source, Free, Freely available, Available for download | biotools:x2k | https://bio.tools/x2k, http://www.maayanlab.net/X2K/ | SCR_016307 | eXpression2Kinases, X2K | 2026-07-30 09:30:01 | 4 | ||||
|
DOMAINATRIX Resource Report Resource Website |
DOMAINATRIX (RRID:SCR_016084) | software resource, software application | Software for protein domain search. It is a part of Embassy software package. | protein, domain, search, molecular, biology | is listed by: Debian | Free, Available for download, Freely available | http://emboss.sourceforge.net/what/, https://sources.debian.org/src/embassy-domainatrix/ | SCR_016084 | Embassy-domainatrix | 2026-07-30 09:29:52 | 0 | ||||||||
|
Ecopcr Resource Report Resource Website 10+ mentions |
Ecopcr (RRID:SCR_016082) | Ecopcr | software resource, software application | Software for Electronic PCR that estimates PCR barcode primers quality and develops new barcode primers. In conjunction with OBITools, users can postprocess ecoPCR output to compute barcode coverage and barcode specificity., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | electronic, PCR, estimate, primers, quality, barcode |
is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_19861 | https://sources.debian.org/src/ecopcr/ | http://www.grenoble.prabi.fr/trac/ecoPCR/ | SCR_016082 | Ecopcr: Electronic polymerase chain reaction | 2026-07-30 09:30:06 | 27 | |||||
|
PyRosetta Resource Report Resource Website 10+ mentions |
PyRosetta (RRID:SCR_018541) | software resource, software application, standalone software | Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions. | Molecular modeling, custom structure prediction, design algorithm, energy function, scoring function, bio.tools |
uses: Python Programming Language is listed by: bio.tools is listed by: Debian is related to: Rosetta has parent organization: Johns Hopkins University; Maryland; USA |
NIGMS R01 GM73151; NIGMS R01 GM078221; NSF 0846324 |
PMID:20061306 | Free, Freely available | biotools:pyrosetta | https://bio.tools/pyrosetta | SCR_018541 | Python Rosetta | 2026-07-30 09:30:24 | 20 | |||||
|
QGIS Resource Report Resource Website 100+ mentions |
QGIS (RRID:SCR_018507) | software resource, software application | Open source cross platform desktop geographic information system application that supports viewing, editing, and analysis of geospatial data. Functions as geographic information system software, allowing users to analyze and edit spatial information, in addition to composing and exporting graphical maps. | Geographic information system, viewing, editing, analysis, geospatial data, spatial information analysis, graphical map, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:QGIS | https://bio.tools/QGIS | SCR_018507 | 2026-07-30 09:30:31 | 400 | ||||||||
|
Clinotator Resource Report Resource Website 1+ mentions |
Clinotator (RRID:SCR_016054) | software resource, software application | Software that performs clinical interpretation of ambiguous ClinVar annotations. This software takes batches of variants as input and queries NCBI eutilities to generate scoring metrics. | clinical, age, weight, score, metric, vcf, python, nbci, annotation, variant, scoring, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free | biotools:clinotator | https://bio.tools/clinotator | SCR_016054 | clinotator.py | 2026-07-30 09:29:58 | 2 | |||||||
|
Bio-ASN1-EntrezGene Resource Report Resource Website |
Bio-ASN1-EntrezGene (RRID:SCR_024056) | software resource, software application | Software regular expression based Perl Parser for NCBI Entrez Gene genome databases. Parses ASN.1-formatted Entrez Gene record and returns data structure that contains all data items from gene record. | Perl parser, NCBI Entrez Gene genome databases parser, ASN.1-formatted Entrez Gene record parser, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-asn1-entrezgene-perl/ | SCR_024056 | libbio-asn1-entrezgene-perl, Bio-ASN1-EntrezGene - Regular expression-based Perl Parser for NCBI Entrez Gene | 2026-07-30 09:31:36 | 0 | ||||||||
|
AcePerl Resource Report Resource Website |
AcePerl (RRID:SCR_024057) | software resource, software application | Software provides an interface to the ACEDB object-oriented database. Both read and write access is provided, and ACE objects are returned as similarly-structured Perl objects. Multiple databases can be opened simultaneously. | software interface, provides interface to ACEDB object-oriented database, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libace-perl/, https://github.com/WormBase/AcePerl | SCR_024057 | Ace, ACE, libace-perl, Ace-Perl, ace-perl, Ace - Object-Oriented Access to ACEDB Databases | 2026-07-30 09:31:54 | 0 | ||||||||
|
shapeit4 Resource Report Resource Website 10+ mentions |
shapeit4 (RRID:SCR_024335) | software resource, software application | Software tool for estimation of haplotypes aka phasing for SNP array and high coverage sequencing data. The version 4 is refactored and improved version of SHAPEIT algorithm with multiple key additional features. | estimation of haplotypes, phasing, SNP array data, high coverage sequencing data, | is listed by: Debian | PMID:31780650 | Free, Available for download, Freely available, | https://sources.debian.org/src/shapeit4/ | SCR_024335 | SHAPEIT, SHAPEIT4 | 2026-07-30 09:31:56 | 21 | |||||||
|
sailfish Resource Report Resource Website 1+ mentions |
sailfish (RRID:SCR_024326) | software resource, software application | Software tool that implements novel, alignment free algorithm for estimation of isoform abundances directly from set of reference sequences and RNA-seq reads. | estimation of isoform abundances, reference sequences, RNA-seq reads, | is listed by: Debian | PMID:24752080 | Free, Available for download, Freely available, | OMICS_03939 | https://sources.debian.org/src/sailfish/ | SCR_024326 | 2026-07-30 09:31:56 | 1 | |||||||
|
ragout Resource Report Resource Website 1+ mentions |
ragout (RRID:SCR_024206) | software resource, software application | Software tool for chromosome level scaffolding using multiple references. Given initial assembly fragments and one or multiple related references it produces chromosome scale assembly. | chromosome level scaffolding, multiple references, produce chromosome scale assembly, | is listed by: Debian | PMID:30341161 | Free, Available for download, Freely available, | OMICS_07883 | SCR_024206 | Reference-Assisted Genome Ordering UTility | 2026-07-30 09:31:45 | 1 | |||||||
|
Bio-SamTools Resource Report Resource Website 1+ mentions |
Bio-SamTools (RRID:SCR_024066) | software resource, software application | Software Perl interface to SamTools library for DNA sequencing. | Perl interface, SamTools library, DNA sequencing, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-samtools-perl/ | SCR_024066 | libbio-samtools-perl | 2026-07-30 09:31:43 | 5 | ||||||||
|
skesa Resource Report Resource Website 1+ mentions |
skesa (RRID:SCR_024341) | software resource, software application | Software de-novo sequence read assembler for microbial genomes.Designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity.SKESA contigs could be connected into GFA graph using GFA connector. | de-novo sequence read assembler, microbial genomes, create breaks at repeat regions in genome, | is listed by: Debian | PMID:30286803 | Free, Available for download, Freely available, | https://sources.debian.org/src/skesa/ | SCR_024341 | SKESA | 2026-07-30 09:31:56 | 8 | |||||||
|
sistr Resource Report Resource Website 10+ mentions |
sistr (RRID:SCR_024342) | SISTR | software resource, software application | SISTR command-line tool. Open web accessible tool for rapidly typing and subtyping draft salmonella genome assemblies. | rapidly typing and subtyping draft salmonella genome assemblies, salmonella genome assemblies, | is listed by: Debian | PMID:26800248 | Free, Available for download, Freely available, | OMICS_12011 | https://sources.debian.org/src/sistr/ | SCR_024342 | Salmonella In Silico Typing Resource | 2026-07-30 09:31:46 | 21 | |||||
|
Bio-SCF Resource Report Resource Website |
Bio-SCF (RRID:SCR_024068) | software resource, software application | Software Perl extension for reading and writting SCF sequence files.This module provides Perl interface to SCF DNA sequencing files. It has both tied hash and an object-oriented interfaces. It provides the ability to read fields from SCF files and limited ability to modify them and write them back. | Perl, Perl extension, reading and writting SCF sequence files, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-scf-perl/ | SCR_024068 | Bio-SCF - Perl extension for reading and writting SCF sequence files, libbio-scf-perl | 2026-07-30 09:31:36 | 0 | ||||||||
|
pufferfish Resource Report Resource Website |
pufferfish (RRID:SCR_024184) | software resource, software application | Software tool implementing novel indexing data structure for compacted de Bruijn graph and colored compacted de Bruijn graph. | indexing data structure, compacted de Bruijn graph, colored compacted de Bruijn graph, | is listed by: Debian | PMID:29949982 | Free, Available for download, Freely available, | https://sources.debian.org/src/pufferfish/ | SCR_024184 | 2026-07-30 09:31:45 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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