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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SeqGene Resource Report Resource Website 1+ mentions |
SeqGene (RRID:SCR_011861) | SeqGene | software resource | An open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, etc. |
is listed by: OMICtools has parent organization: SourceForge |
Open unspecified license | OMICS_01134 | SCR_011861 | SciCrunch Registry | 2026-10-24 12:46:41 | 2 | |||||||||
|
naiveBayesCall Resource Report Resource Website |
naiveBayesCall (RRID:SCR_011866) | naiveBayesCall | software resource | An efficient model-based base-calling algorithm for high-throughput sequencing. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_01152, biotools:bayescall | https://bio.tools/bayescall | SCR_011866 | SciCrunch Registry | 2026-10-24 12:46:41 | 0 | ||||||||
|
Scalpel Resource Report Resource Website 50+ mentions |
Scalpel (RRID:SCR_012107) | software resource | A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina). | software package, c++, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25128977 | biotools:scalpel, OMICS_05395 | https://bio.tools/scalpel | SCR_012107 | SciCrunch Registry | 2026-10-24 12:46:46 | 62 | ||||||||
|
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 | SciCrunch Registry | 2026-10-24 12:46:46 | 57 | |||||||
|
ReviSTER Resource Report Resource Website |
ReviSTER (RRID:SCR_012113) | software resource | Software for an automated pipeline using a ''local mapping reference reconstruction method'' to revise mismapped or partially misaligned reads at simple tandem repeat loci. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23677944 | GNU General Public License | OMICS_05468 | SCR_012113 | SciCrunch Registry | Revise Simple Tandem repeat Error Reads | 2026-10-24 12:46:46 | 0 | |||||||
|
SNP ratio test Resource Report Resource Website 1+ mentions |
SNP ratio test (RRID:SCR_012070) | software resource | Software to calculate the number of significant SNPs in pathway divided by the number of SNPs in pathway. | standalone software, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19620097 | GNU General Public License | biotools:snp_ratio_test, OMICS_04390 | https://bio.tools/snp_ratio_test | SCR_012070 | SciCrunch Registry | 2026-10-24 12:46:45 | 2 | |||||||
|
VirVarSeq Resource Report Resource Website 10+ mentions |
VirVarSeq (RRID:SCR_012116) | software resource | Software for a low frequency Virus Variant detection pipeline for Illumina data. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25178459 | OMICS_05534 | SCR_012116 | SciCrunch Registry | 2026-10-24 12:46:46 | 13 | |||||||||
|
Toxtree Resource Report Resource Website 100+ mentions |
Toxtree (RRID:SCR_012086) | software resource | A full-featured and flexible user-friendly open source software application, which is able to estimate toxic hazard by applying a decision tree approach. | standalone software, web app |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18853299 | OMICS_05024 | SCR_012086 | SciCrunch Registry | 2026-10-24 12:46:45 | 109 | |||||||||
|
Viewmol Resource Report Resource Website |
Viewmol (RRID:SCR_012088) | software resource | Software providing a graphical front end for computational chemistry programs. | standalone software, windows, c, python |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
GNU General Public License | OMICS_05057 | https://sources.debian.org/src/viewmol/ | SCR_012088 | SciCrunch Registry | 2026-10-24 12:46:46 | 0 | ||||||||
|
Toxmatch Resource Report Resource Website 1+ mentions |
Toxmatch (RRID:SCR_012087) | software resource | A software tool to facilitate chemical similarity calculations. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18617309 | OMICS_05025 | SCR_012087 | SciCrunch Registry | 2026-10-24 12:46:45 | 2 | |||||||||
|
QuteMol Resource Report Resource Website 10+ mentions |
QuteMol (RRID:SCR_012089) | software resource | Open source (GPL) software providing an interactive, high quality molecular visualization system. | standalone software, unix/linux, windows |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:17080857 DOI:10.1109/TVCG.2006.115 |
Free, Freely available | OMICS_05075 | https://sources.debian.org/src/qutemol/ | SCR_012089 | SciCrunch Registry | 2026-10-24 12:46:45 | 14 | |||||||
|
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 | SciCrunch Registry | Modular Application Toolkit for Chromatography Mass-Spectrometry | 2026-10-24 12:46:45 | 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 | SciCrunch Registry | Frequency-based Insilico Genome Generator | 2026-10-24 12:46:45 | 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 | SciCrunch Registry | Do-It-Yourself Annotator | 2026-10-24 12:46:45 | 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 | SciCrunch Registry | 2026-10-24 12:46:45 | 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 | SciCrunch Registry | 2026-10-24 12:46:45 | 10714 | |||||||
|
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 | SciCrunch Registry | 2026-10-24 12:46:46 | 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 | SciCrunch Registry | 2026-10-24 12:46:46 | 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 | SciCrunch Registry | 2026-10-24 12:46:45 | 34 | |||||||||
|
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 | SciCrunch Registry | Connecting Overlapped Pair-End | 2026-10-24 12:46:46 | 3 |
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