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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Protein Databank Fun Resource Report Resource Website 1+ mentions |
Protein Databank Fun (RRID:SCR_008226) | data processing software, software application, software resource, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. PDBfun is a web server for structural and functional analysis of proteins at the residue level. pdbFun gives fast access to the whole Protein Data Bank (PDB) organized as a database of annotated residues. The available data (features) range from solvent exposure to ligand binding ability, location in a protein cavity, secondary structure, residue type, sequence functional pattern, protein domain and catalytic activity. PDBfun is an integrated web tool for querying the PDB at the residue level and for local structural comparison. It integrates knowledge on single residues in protein structures coming from other databases or calculated with available or in-house developed instruments for structural analysis. Each set of different annotations represents a feature. Features are listed in PDBfun main page in orange. Features can be used for building residues selections. | functional, 2d, ability, activity, analysis, binding, catalytic, cavity, chain, cleft, domain, ligand, location, motif, protein, protein structure databases, residue, secondary, sequence, size, solvent, structural, structure, surface | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21315 | SCR_008226 | PDBfun | 2026-08-04 09:42:07 | 2 | |||||||||
|
GMAP Resource Report Resource Website 500+ mentions |
GMAP (RRID:SCR_008992) | GMAP | data processing software, source code, alignment software, software resource, software application, image analysis software | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A software program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing. | mrna, est sequence, expressed sequence tag, sequence, cdna sequence, genome, cdna, bio.tools |
is used by: deFuse is listed by: Debian is listed by: bio.tools has parent organization: Genentech |
PMID:15728110 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_15072, biotools:gmap, nlx_152505 | https://bio.tools/gmap, https://sources.debian.org/src/gmap/ | SCR_008992 | 2026-08-04 09:42:16 | 594 | ||||||
|
CMAP Resource Report Resource Website 100+ mentions |
CMAP (RRID:SCR_009034) | CMap | data processing software, software application, software resource, data analysis software | Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, unix, solaris, freebsd, linux, sequence, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite has parent organization: Generic Model Organism Database Project works with: Drug Gene Budger |
PMID:19648141 | GNU General Public License | nlx_153998, OMICS_00933 | https://sourceforge.net/projects/gmod/files/cmap/ | http://www.gmod.org/cmap/, http://gmod.org/wiki/Cmap | SCR_009034 | , GMOD Comparative Mapping (CMap) tool, Comparative Mapping tool, genetic and comparative maps | 2026-08-04 09:42:17 | 413 | ||||
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Hypermut Resource Report Resource Website 100+ mentions |
Hypermut (RRID:SCR_014933) | data processing software, data analysis software, software resource, sequence analysis software, software application, web application | Web application for the analysis and detection of APOBEC-induced hypermutations. The first sequence in the input alignment will be used as the reference sequence, and each of the other sequences will be used as a query sequence. | mutation, hypermutation, sequence, sequence analysis software genome, web application | PMID:10869039 | SCR_014933 | Hypermut 2.0 | 2026-08-04 09:43:34 | 124 | ||||||||||
|
Seq-Gen Resource Report Resource Website 100+ mentions |
Seq-Gen (RRID:SCR_014934) | simulation software, software application, software resource | Software program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. | simulator, simulation software, molecular evolution, nucleotide, amino acid, sequence, phylogeny, phylogenetic tree |
is listed by: Debian is listed by: OMICtools has parent organization: University of Edinburgh; Scotland; United Kingdom |
Wellcome Trust ; BBSRC ; Fogarty ; The Royal Society |
DOI:10.1093/bioinformatics/13.3.235 | Available for download | OMICS_15373 | https://sources.debian.org/src/seq-gen/ | SCR_014934 | 2026-08-04 09:43:33 | 155 | ||||||
|
MacVector Resource Report Resource Website 1000+ mentions |
MacVector (RRID:SCR_015700) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, agarose gel simulation and a variety of other functions. | vector, sequence, sequence alignment, sequence editing, primer design, phylogenetic reconstruction, FASEB list | Commercially available, Available for purchase, Runs on Mac OS, Free version available | SCR_015700 | 2026-08-04 09:43:43 | 1496 | |||||||||||
|
Ariba Resource Report Resource Website 100+ mentions |
Ariba (RRID:SCR_015976) | data processing software, data analysis software, software resource, sequence analysis software, software application, software toolkit | Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling. | software, analysis, tool, sequence, antibiotic, resistance, assembly, local, mlst |
is listed by: Debian is listed by: OMICtools |
Wellcome Trust 206194; Biotechnology and Biological Sciences Research Council BB/M014088/1 |
PMID:29177089 DOI:10.1099/mgen.0.000131 |
Free, Available for download, Freely available | OMICS_17327 | https://sources.debian.org/src/artemis/ | SCR_015976 | 2026-08-04 09:43:47 | 197 | ||||||
|
Atac Resource Report Resource Website 1000+ mentions |
Atac (RRID:SCR_015980) | data processing software, alignment software, data analysis software, software resource, sequence analysis software, software application, image analysis software | Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences. | software, tool, DNA, sequence, analysis, aligning, genome, compare, mapping, assembly, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btr285 | Free, Freely available, Available for download | OMICS_29044, biotools:atac | https://bio.tools/atac, https://sources.debian.org/src/atac/ | SCR_015980 | 2026-08-04 09:43:47 | 1748 | |||||||
|
Axe Resource Report Resource Website 1+ mentions |
Axe (RRID:SCR_015984) | data processing software, data analysis software, software resource, sequence analysis software, software application, software toolkit | Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples. | software, tool, sequence, analysis, barcode, demultiplexing |
is listed by: Debian is listed by: OMICtools |
Free, Freely available, Available for download | OMICS_19788 | https://readthedocs.org/projects/axe-demultiplexer/, https://sources.debian.org/src/baitfisher/ | SCR_015984 | Axe-demultiplexer | 2026-08-04 09:43:47 | 1 | |||||||
|
Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | data processing software, data analysis software, data management software, software resource, software application, software toolkit | Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies. | c++, api, sam, bam genome, sequence, alignment, data, analysis, management, command, manipulation, binary, map, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG004719; NHGRI RC2 HG005552 |
PMID:21493652 DOI:10.1093/bioinformatics/btr174 |
biotools:bamtools, OMICS_11315 | https://bio.tools/bamtools, https://sources.debian.org/src/bamtools/ | SCR_015987 | API:Application Programming Interface, BAM:Binary Alignment Map, SAM:Sequence Alignment Map | 2026-08-04 09:43:47 | 324 | ||||||
|
Blixem Resource Report Resource Website 1+ mentions |
Blixem (RRID:SCR_015994) | data processing software, alignment software, software resource, software application, image analysis software | Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites. | software, sequence, alignment, annotation, genomic, reference, data, display, manipulation, DNA |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust Grant 098051; NHGRI U54 HG00455 |
PMID:26801397 | Free, Available for download | SCR_015994 | SEQtools Blixem | 2026-08-04 09:43:47 | 2 | |||||||
|
ALTER Resource Report Resource Website 100+ mentions |
ALTER (RRID:SCR_015968) | data processing software, alignment software, data analysis software, software resource, sequence analysis software, software application, image analysis software, web application | Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats. | Alignment conversion, genome, sequence, DNA, protein, format alignment, phylogenetics, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
European Research Council ERC-2007-Stg 203161-PHYGENOM to D.P.; Spanish Ministry of Science and Education BFU2009-08611 to D.P.; Xunta de Galicia PGIDIT07PXIB310202PR to D.P.; INBIOMED initiative ; University of Vigo 09VIB10 to F.F-.R. |
PMID:20439312 DOI:10.1093/nar/gkq321 |
Freely available, Free, Available for download | OMICS_19786, biotools:alter | https://github.com/sing-group/ALTER, https://bio.tools/alter, https://sources.debian.org/src/alter-sequence-alignment/ | SCR_015968 | ALTER: ALignment Transformation EnviRonment, ALignment Transformation EnviRonment | 2026-08-04 09:43:46 | 112 | |||||
|
AMAP Resource Report Resource Website 100+ mentions |
AMAP (RRID:SCR_015969) | data processing software, source code, alignment software, software resource, software application, image analysis software | Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method. | software, peptide, sequence, alignment, annealing, bioinformatics, multiple, svn, posterior, decoding |
is listed by: Debian is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
NSF EF 03-31494; NHGRI R01 HG2362; NSF CCF0347992 |
PMID:17237099 DOI:10.1093/bioinformatics/btl311 |
Free, Available for download | OMICS_19787 | http://baboon.math.berkeley.edu/amap/, https://sources.debian.org/src/amap-align/ | https://sources.debian.org/src/amos-assembler/ | SCR_015969 | amap-align | 2026-08-04 09:43:46 | 388 | ||||
|
Aragorn Resource Report Resource Website 100+ mentions |
Aragorn (RRID:SCR_015974) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software that detects tRNA genes and tmRNA genes in nucleotide sequences. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base‐paired cloverleaf., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | software, program, nucleotide, sequence, detect, tmRNA, tRNA |
is listed by: Debian is listed by: OMICtools |
PMID:14704338 DOI:10.1093/nar/gkh152 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04227 | https://sources.debian.org/src/arden/ | SCR_015974 | 2026-08-04 09:43:47 | 472 | |||||||
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Poretools Resource Report Resource Website 50+ mentions |
Poretools (RRID:SCR_015879) | data processing software, data analysis software, software resource, sequence analysis software, software application, software toolkit | Software toolkit for analyzing nanopore sequence data. | nanopore, sequence, python, oxford nanopore, MinION, quality control, downstream analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
Medical Research Council ; NHGRI R01 HG006693 |
PMID:25143291 | Open source, Free, Available for download | biotools:poretools | https://bio.tools/poretools | SCR_015879 | 2026-08-04 09:43:44 | 81 | ||||||
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G-Anchor Resource Report Resource Website 1+ mentions |
G-Anchor (RRID:SCR_016046) | G-Anchor | data processing software, alignment software, data analysis software, software resource, sequence analysis software, software application, image analysis software | Software for comparing large genomes and exploiting highly conserved sequences as evolutionary-stable "anchors". The pipeline maps a newly sequenced genome (assembled in scaffolds) on a reference genome without the need of a supercomputer. | anchor, comparison, scaffold, whole genome, alignment, sequence, mapping, anchoring, highly conserved elements, hce, evolution | HPC Wales ; Biotechnology and Biological Sciences Research Council BB/J010170/1 |
Free, Available for download | SCR_016046 | G-Anchor: A novel approach for cross-species comparison | 2026-08-04 09:43:48 | 1 | ||||||||
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HiLive Resource Report Resource Website |
HiLive (RRID:SCR_016134) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software tool for performing read mapping that maps Illumina HiSeq sequencer read alignments when they are produced. Used in Next Generation Sequencing in time critical, clinical applications. | perform, read, mapping, sequence, alignment, analysis, Illumina, time, critical, clinical, application |
is listed by: Debian is listed by: OMICtools |
the German Federal Ministry of Health IIA5-2512-FSB-725 | PMID:27794555 | Free, Available for download | OMICS_13393 | https://sources.debian.org/src/hilive/ | https://sourceforge.net/projects/hilive/ | SCR_016134 | 2026-08-04 09:43:49 | 0 | |||||
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FSA Resource Report Resource Website 1+ mentions |
FSA (RRID:SCR_016114) | FSA | data processing software, alignment software, software resource, software application, image analysis software | Software for a statistical multiple sequence alignment algorithm which uses a "distance-based" approach to align homologous protein, RNA or DNA sequences. The GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned. | multiple, sequence, alignment, algorithm, distance, approach, homologous, protein, DNA, RNA, acurate, fast |
is listed by: Debian is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
PMID:19478997 | Free, available for download | https://sources.debian.org/src/fsa/ | SCR_016114 | Fast Statistical Alignment, FSA: Fast Statistical Alignment | 2026-08-04 09:43:49 | 3 | ||||||
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GARLI Resource Report Resource Website 100+ mentions |
GARLI (RRID:SCR_016117) | GARLI | data processing software, software application, software resource, data analysis software | Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution. | inference, phylogenetic, tree, analysis, molecular, sequence, data, maximum, likelihood, criterion, nucleotide, amino acid, codon, model, evolution |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_04234 | https://code.google.com/archive/p/garli/, https://sources.debian.org/src/garli/ | SCR_016117 | Genetic Algorithm for Rapid Likelihood Inference | 2026-08-04 09:43:49 | 279 | ||||||
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Fsm-lite Resource Report Resource Website 10+ mentions |
Fsm-lite (RRID:SCR_016115) | data processing software, software application, software resource, data analysis software | Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data. | protein, dna, rna, sequence, analysis, core, implementation, frequency, based, substring, mining, extract, discriminate, dataset, sequencing, high throughput |
is listed by: Debian is listed by: OMICtools |
Free, Available for download | OMICS_28406 | https://sources.debian.org/src/fsm-lite/ | SCR_016115 | fsm, Frequency-based String Mining, Frequency-based String Mining (lite) | 2026-08-04 09:43:49 | 15 |
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