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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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mPTP Resource Report Resource Website 1+ mentions |
mPTP (RRID:SCR_024121) | software resource, data processing software, software application, data analysis software | Software tool for single locus species delimitation. Implements fast method to compute the ML delimitation from inferred phylogenetic tree of the samples.Used to handle very large biodiversity datasets. | single locus species delimitation, ML delimitation from inferred phylogenetic tree of the samples, ML delimitation, inferred phylogenetic tree, samples inferred phylogenetic tree, | is listed by: Debian | PMID:28108445 | Free, Available for download, Freely available, | OMICS_15264 | https://sources.debian.org/src/mptp/ | SCR_024121 | , mptp, multi-rate Poisson Tree Processes | 2026-08-05 10:47:58 | 1 | ||||||
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MRtrix3 Resource Report Resource Website 100+ mentions |
MRtrix3 (RRID:SCR_024123) | software resource, data processing software, software application, data analysis software | Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses. | diffusion MRI analyses, tractography, next generation group level analyses, | is listed by: Debian | PMID:31473352 | Free, Available for download, Freely available, | https://sources.debian.org/src/mrtrix3/ | SCR_024123 | mrtrix3 | 2026-08-05 10:47:58 | 185 | |||||||
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CTSim Resource Report Resource Website |
CTSim (RRID:SCR_024004) | software application, simulation software, software resource | Software tool to simulate process of transmitting X-rays through phantom objects. Reconstructs original phantom image from projections. Has wide array of image analysis and image processing functions. | Computed tomography simulator, reconstruct original phantom image from projections, reconstruct image, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ctsim/ | SCR_024004 | ctsim, Open Source Computed Tomography Simulator | 2026-08-05 10:47:56 | 0 | ||||||||
|
MIA Resource Report Resource Website |
MIA (RRID:SCR_024081) | software resource, image analysis software, software application, data processing software | Software toolkit for gray scale medical image analysis. Provides combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in command shell and prototype algorithms as shell scripts. MIA is build around a plug-in structure that makes it easy to add functionality without compromising the original code base, and it makes use of wide variety of external libraries that provide additional functionality. | gray scale medical image analysis, interactive image processing, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/mia/ | https://sources.debian.org/src/libmialm/ | SCR_024081 | python3-mia, libmia-2.4-dev, mia-tools, mia-viewit, libvistaio-dev, libmialm-dev, libmiaviewit-dev, libmialm, mialmpick | 2026-08-05 10:47:58 | 0 | |||||||
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sigma-align Resource Report Resource Website |
sigma-align (RRID:SCR_024337) | data processing software, image analysis software, software application, alignment software, software resource | Software alignment program with new algorithm and scoring scheme designed specifically for non-coding DNA sequence. This problem is now growing in importance with the increasing number of fully-sequenced species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms (such as PhyloGibbs) for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step. | alignment program, non-coding DNA sequence, | is listed by: Debian | PMID:16542424 | Free, Available for download, Freely available, | OMICS_29594 | https://sources.debian.org/src/sigma-align/ | SCR_024337 | Simple greedy multiple alignment | 2026-08-05 10:48:02 | 0 | ||||||
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signalalign Resource Report Resource Website 1+ mentions |
signalalign (RRID:SCR_024339) | data processing software, image analysis software, software application, alignment software, software resource | Software tool to align ionic current from MinION to reference sequence using trainable hidden Markov model. HMM-HDP models for MinION signal alignments, | Oxford Nanopore Technologies, MinION sequences DNA, align ionic current, reference sequence, trainable hidden Markov model, HMM-HDP models, MinION signal alignments, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/signalalign/ | SCR_024339 | 2026-08-05 10:48:03 | 2 | |||||||||
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toppred Resource Report Resource Website 1+ mentions |
toppred (RRID:SCR_024385) | software application, simulation software, software resource | Software tool for membrane protein structure prediction.Transmembrane topology prediction.Used for predicting topology of bacterial inner membrane proteins. | Membrane protein structure prediction, transmembrane topology prediction, predicting topology, bacterial inner membrane proteins topology prediction, | is listed by: Debian | PMID:1593632 | Free, Available for download, Freely available, | OMICS_07268 | https://sources.debian.org/src/toppred/ | SCR_024385 | 2026-08-05 10:48:02 | 3 | |||||||
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Tn-seq explorer Resource Report Resource Website 1+ mentions |
Tn-seq explorer (RRID:SCR_024387) | software resource, data processing software, software application, data analysis software | Software package written in Java for analysis of high-throughput sequencing data of transposon mutant libraries.Reads the alignment and the gene annotation, and provides the user with set of tools to investigate data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions. | high-throughput sequencing data analysis, transposon mutant libraries, read alignment and gene annotation, identify genes, low counts of transposon insertions genes, | is listed by: Debian | PMID:25938432 | Free, Available for download, Freely available, | https://sources.debian.org/src/tn-seqexplorer/ | SCR_024387 | , Tn-seq Explorer, tn-seqexplorer | 2026-08-05 10:48:03 | 3 | |||||||
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TRANSIT Resource Report Resource Website 1+ mentions |
TRANSIT (RRID:SCR_024389) | software resource, data processing software, software application, data analysis software | Software tool for Himar1 TnSeq analysis.Provides graphical interface to three different statistical methods for analyzing TnSeq data. Used for identifying essential genes in individual datasets as well as comparative analysis between conditions. | Himar1 TnSeq data analysis, identifying essential genes in individual datasets, comparative analysis between conditions, | is listed by: Debian | PMID:26447887 | Free, Available for download, Freely available, | OMICS_10215 | https://sources.debian.org/src/tnseq-transit/ | SCR_024389 | tnseq-transit | 2026-08-05 10:48:02 | 1 | ||||||
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TREE-PUZZLE Resource Report Resource Website 1+ mentions |
TREE-PUZZLE (RRID:SCR_024382) | software resource, data processing software, software application, data analysis software | Software tool to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. Allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Computes pairwise maximum likelihood distances as well as branch lengths for user specified trees.Conducts statistical tests on the data set. | reconstruct phylogenetic trees, molecular sequence data, maximum likelihood, compute pairwise maximum likelihood distances, conduct statistical tests, data analysis, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_18458 | https://sources.debian.org/src/tree-puzzle/ | https://sources.debian.org/src/tree-ppuzzle/ | SCR_024382 | tree-puzzle | 2026-08-05 10:48:03 | 3 | ||||||
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sparta Resource Report Resource Website 1+ mentions |
sparta (RRID:SCR_024349) | software resource, data processing software, software application, data analysis software | Software workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms. | analyzing single-end Illumina RNA-seq data, | is listed by: Debian | PMID:26847232 | Free, Available for download, Freely available, | https://sources.debian.org/src/sparta/ | SCR_024349 | SPARTA | 2026-08-05 10:48:02 | 9 | |||||||
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Yanosim Resource Report Resource Website |
Yanosim (RRID:SCR_024363) | Yanosim | software application, simulation software, software resource | Software tool as read simulator for nanopore DRS datasets. | read simulator for nanopore DRS datasets, read simulator, nanopore DRS datasets, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/yanosim/ | SCR_024363 | yanosim, yet another nanopore simulator | 2026-08-05 10:48:02 | 0 | |||||||
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SPAdes Resource Report Resource Website 100+ mentions |
SPAdes (RRID:SCR_000131) | SPAdes | software toolkit, software resource | Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | assembler, single, cell, small, genome, short, read, data |
is used by: shovill is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: rnaSPAdes is related to: rnaQUAST has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia works with: Illumina: iSeq 100 Sequencing System |
Government of the Russian Federation ; NCRR P41 RR024851 |
PMID:24093227 PMID:22506599 DOI:10.1089/cmb.2012.0021 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01502 | https://sources.debian.org/src/spades/ | http://bioinf.spbau.ru/spades/ | SCR_000131 | SPAdes Genome Assembler | 2026-08-05 10:43:06 | 101 | |||
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Mspire-Simulator Resource Report Resource Website 1+ mentions |
Mspire-Simulator (RRID:SCR_001431) | software application, simulation software, standalone software, software resource | A free, open-source shotgun proteomic simulator that goes beyond previous simulation attempts by generating LC-MS features with realistic m/z and intensity variance along with other noise components. | standalone software, shotgun, proteomic, simulation software, bio.tools |
uses: mzML is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: Brigham Young University; Utah; USA |
PMID:24090032 | Free, Freely Available | biotools:mspire-simulator, OMICS_03359 | https://bio.tools/mspire-simulator | SCR_001431 | 2026-08-05 10:43:22 | 1 | |||||||
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amide Resource Report Resource Website 100+ mentions |
amide (RRID:SCR_005940) | AMIDE | data processing software, software application, image analysis software, software resource | Software tool for viewing, analyzing, and registering volumetric medical imaging data sets. It has been written on top of GTK+ and runs on any system that supports this toolkit (Linux, Windows, Mac OS X, etc.). The program incorporates automatic non-orthogonal data reslicing, allowing multiple data set to be fused without imposed constraints on the dimensions, anisotrophy, or voxel sizes of the data. Additional features include 3D ROI (ellipses, cylinders, boxes, and isocontours), multi-slice viewing, volume rendering, and data importing through the (X)MedCon library. | volumetric medical imaging data, data analysis, data visualization, non-orthogonal data |
is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:14649056 | Free, Freely available | nif-0000-00261 | https://sources.debian.org/src/amide/ | SCR_005940 | , a medical image data examiner, A Medical Image Data Examiner | 2026-08-05 10:44:24 | 472 | |||||
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IMG System Resource Report Resource Website 100+ mentions |
IMG System (RRID:SCR_002965) | IMG, IMG/M | data or information resource, portal | Resource for analysis and annotation of genome and metagenome datasets in comprehensive comparative context. IMG provides users with tools for analyzing publicly available genome datasets and metagenome datasets. | microbiome, microbial genetics, genome and metagenome datasets analysis, genome and metagenome datasets, genome, metagenomics, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: Human Microbiome Project has parent organization: DOE Joint Genome Institute |
PMID:17932063 PMID:22086953 |
Free, Freely available | nif-0000-03010, OMICS_01478, SCR_014605, biotools:img_m | http://img.jgi.doe.gov/m, https://bio.tools/img_m | SCR_002965 | Integrated Microbial Genomes System | 2026-08-05 10:43:44 | 199 | |||||
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Populations Resource Report Resource Website |
Populations (RRID:SCR_024175) | software toolkit, software library, software resource | Population genetic software for individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions. | Population genetic, individuals or populations distances, allelic frequencies, phylogenetic trees, file conversions, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_29592 | https://sources.debian.org/src/populations/ | SCR_024175 | populations | 2026-08-05 10:47:59 | 0 | |||||||
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quicktree Resource Report Resource Website 10+ mentions |
quicktree (RRID:SCR_024205) | software toolkit, software library, software resource | Software application as implementation of Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments. | Neighbor-Joining algorithm, reconstructing phylogenies from huge alignments, | is listed by: Debian | PMID:3447015 | Free, Available for download, Freely available, | https://sources.debian.org/src/quicktree/ | SCR_024205 | 2026-08-05 10:47:59 | 12 | ||||||||
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pycoqc Resource Report Resource Website 10+ mentions |
pycoqc (RRID:SCR_024185) | software toolkit, software resource | Software application to compute metrics and generate interactive QC plots for Oxford Nanopore technologies sequencing data. | compute metrics, generate interactive QC plots, Oxford Nanopore technologies sequencing data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pycoqc/ | SCR_024185 | 2026-08-05 10:47:59 | 18 | |||||||||
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python-airr Resource Report Resource Website |
python-airr (RRID:SCR_024187) | software toolkit, software library, software resource | Software airr reference library provides basic functions and classes for interacting with AIRR Community Data Representation Standards, including tools for read, write and validation. | airr reference library, functions and classes for interacting with AIRR Community Data Representation Standards, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/python3-airr/ | SCR_024187 | 2026-08-05 10:48:00 | 0 |
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