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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Maltcms Resource Report Resource Website |
Maltcms (RRID:SCR_012057) | software resource | An application framework mainly suited for developers working in the domain of bioinformatics for metabolomics and proteomics. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_03356 | SCR_012057 | Modular Application Toolkit for Chromatography Mass-Spectrometry | 2026-02-14 02:02:33 | 0 | ||||||||||
|
FIGG Resource Report Resource Website 1+ mentions |
FIGG (RRID:SCR_012064) | software resource | A large-scale whole genome simulation tool which generates large numbers of whole genomes with known sequence characteristics based on direct sampling of experimentally known or theorized variations. | standalone software, unix/linux, mac os x, windows, java, mapreduce |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24885193 | Free, Public | OMICS_04164 | SCR_012064 | Frequency-based Insilico Genome Generator | 2026-02-14 02:02:09 | 3 | |||||||
|
DIYA Resource Report Resource Website 10+ mentions |
DIYA (RRID:SCR_012066) | software resource | A modular and configurable open source pipeline software, written in Perl, used for the rapid annotation of bacterial genome sequences. | standalone software, c++, java, perl, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19254921 | GNU General Public License | OMICS_04221 | SCR_012066 | Do-It-Yourself Annotator | 2026-02-14 02:02:17 | 10 | |||||||
|
Fastphylo Resource Report Resource Website 1+ mentions |
Fastphylo (RRID:SCR_012068) | software resource | A software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing a phylogeny from a distance matrix. | applet |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24255987 | OMICS_04248 | SCR_012068 | 2026-02-14 02:02:09 | 2 | |||||||||
|
MrBayes Resource Report Resource Website 10000+ mentions |
MrBayes (RRID:SCR_012067) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. | applet, mac os x, unix/linux, windows |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:22357727 DOI:10.1093/sysbio/sys029 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04237 | https://sources.debian.org/src/mrbayes/ | SCR_012067 | 2026-02-14 02:02:34 | 10711 | |||||||
|
MMAX2 Resource Report Resource Website 1+ mentions |
MMAX2 (RRID:SCR_012100) | software resource | A GUI-based text annotation tool for creating and visualizing annotations. | applet, java |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_05235 | SCR_012100 | 2026-02-14 02:02:18 | 1 | ||||||||||
|
iPapers Resource Report Resource Website |
iPapers (RRID:SCR_012103) | software resource | Software application that manages many PDF files of articles, whose information can be obtained by PubMed. | standalone software, mac os x |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_05280 | SCR_012103 | 2026-02-14 02:02:35 | 0 | ||||||||||
|
PhyloTreePruner Resource Report Resource Website 10+ mentions |
PhyloTreePruner (RRID:SCR_012069) | software resource | A utility that uses a phylogenetic approach to refine orthology inferences made by graph-based (or other) methods. | applet |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24250218 | OMICS_04250 | SCR_012069 | 2026-02-14 02:02:34 | 32 | |||||||||
|
Connecting Overlapped Pair-End reads Resource Report Resource Website 1+ mentions |
Connecting Overlapped Pair-End reads (RRID:SCR_012102) | COPE | software resource | An efficient software tool to connect overlapping pair-end reads using k-mer frequencies. | standalone software, c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23044551 | GNU General Public License, v3 | OMICS_05256 | ftp://ftp.genomics.org.cn/pub/cope | SCR_012102 | Connecting Overlapped Pair-End | 2026-02-14 02:02:10 | 3 | |||||
|
RASP Resource Report Resource Website 100+ mentions |
RASP (RRID:SCR_012062) | software resource | Software that uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy. | standalone software, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24445369 | OMICS_03392 | SCR_012062 | 2026-02-14 02:02:17 | 323 | |||||||||
|
GSim Resource Report Resource Website 1+ mentions |
GSim (RRID:SCR_012061) | software resource | Free software tool for visualisation and processing of experimental and simulated nuclear magnetic resonance (NMR) spectra. | standalone software, c++ |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License | OMICS_03390 | SCR_012061 | 2026-02-14 02:02:33 | 7 | |||||||||
|
Scramble Resource Report Resource Website 10+ mentions |
Scramble (RRID:SCR_012036) | software resource | A C software implementation of SAM, BAM and CRAM file I/O. | standalone software, c, c++, fortran |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24930138 | BSD License | OMICS_04662 | SCR_012036 | 2026-02-14 02:02:17 | 21 | ||||||||
|
CowCoDA Resource Report Resource Website |
CowCoDA (RRID:SCR_012039) | software resource | Software that performs retention time alignment on the given set of peaks. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18715018 | OMICS_02380 | SCR_012039 | 2026-02-14 02:02:33 | 0 | |||||||||
|
OpenMS Resource Report Resource Website 100+ mentions |
OpenMS (RRID:SCR_012042) | software resource | An algorithm to align LC-MS samples and to match corresponding ion species across samples. | standalone software, mac os x, unix/linux, windows, c++, python, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:17646306 DOI:10.1186/1471-2105-9-163 |
GNU Lesser General Public License | biotools:openms | https://bio.tools/openms https://sources.debian.org/src/openms/ |
SCR_012042 | 2026-02-14 02:02:17 | 174 | |||||||
|
OBI-Warp Resource Report Resource Website 1+ mentions |
OBI-Warp (RRID:SCR_012041) | software resource | Software that aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:16944896 | MIT License | OMICS_02386, biotools:obi-warp | https://bio.tools/obi-warp | SCR_012041 | Ordered Bijective Interpolated Warping | 2026-02-14 02:02:33 | 2 | ||||||
|
TOPP Resource Report Resource Website 10+ mentions |
TOPP (RRID:SCR_012044) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on May 23rd,2023. Software that provides a set of computational tools which can be easily combined into analysis pipelines even by non-experts and can be used in proteomics workflows. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:17237091 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02451 | SCR_012044 | 2026-02-14 02:02:09 | 25 | ||||||||
|
Antilope Resource Report Resource Website 1+ mentions |
Antilope (RRID:SCR_012046) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23rd,2023. Software that combines Lagrangian relaxation for solving an integer linear programming formulation with an adaptation of Yen''s k shortest paths algorithm. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21464512 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02481 | SCR_012046 | 2026-02-14 02:02:17 | 4 | ||||||||
|
swissPIT Resource Report Resource Website |
swissPIT (RRID:SCR_012045) | software resource | Software for pipelined analysis of mass spectrometry data. |
is listed by: OMICtools has parent organization: SourceForge has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:18436540 | GNU General Public License | OMICS_02452 | SCR_012045 | Swiss Protein Identification Toolbox | 2026-02-14 02:02:33 | 0 | ||||||||
|
ICPL ESIQuant Resource Report Resource Website |
ICPL ESIQuant (RRID:SCR_012047) | software resource | A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23454610 | biotools:icpl_esiquant, OMICS_02490 | https://bio.tools/icpl_esiquant | SCR_012047 | 2026-02-14 02:02:34 | 0 | ||||||||
|
MToolBox Resource Report Resource Website 50+ mentions |
MToolBox (RRID:SCR_012112) | software resource | Software for a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25028726 | GNU General Public License | OMICS_05466, biotools:mtoolbox | https://bio.tools/mtoolbox | SCR_012112 | 2026-02-14 02:02:18 | 56 |
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