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https://qtlreaper.sourceforge.net/
Software, written in C and compiled as Python module, for rapidly scanning microarray expression data for Quantitative Trait Locies. Searches for association between each expression trait and all genotypes and evaluates that association by permutation test. Performs bootstrap resampling to estimate confidence region for location of putative QTL.
Proper citation: qtlreaper (RRID:SCR_024199) Copy
https://mhap.readthedocs.io/en/stable/
Software tool as reference implementation of probabilistic sequence overlapping algorithm. Used to detect overlaps between noisy long-read sequence data.
Proper citation: MHAP (RRID:SCR_024113) Copy
https://github.com/GATB/MindTheGap
Software tool to perform detection and assembly of DNA insertion variants in NGS read datasets with respect to reference genome.Used to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome.
Proper citation: MindTheGap (RRID:SCR_024115) Copy
https://jydu.github.io/maffilter/
Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc.
Proper citation: MafFilter (RRID:SCR_024105) Copy
https://sparta.readthedocs.io/en/latest/
Software workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms.
Proper citation: sparta (RRID:SCR_024349) Copy
http://maude.cs.illinois.edu/w/index.php/The_Maude_System
Software high performance reflective language and system supporting both equational and rewriting logic specification and programming for wide range of applications.Supports equational specification and programming, rewriting logic computation.
Proper citation: Maude (RRID:SCR_024108) Copy
https://github.com/Pas-Kapli/mptp
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.
Proper citation: mPTP (RRID:SCR_024121) Copy
https://github.com/bartongroup/yanosim
Software tool as read simulator for nanopore DRS datasets.
Proper citation: Yanosim (RRID:SCR_024363) Copy
http://ugovaretto.github.io/molekel/
Open source multi platform molecular visualization program.
Proper citation: Molekel (RRID:SCR_024122) Copy
Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.
Proper citation: MRtrix3 (RRID:SCR_024123) Copy
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.
Proper citation: MIA (RRID:SCR_024081) Copy
https://cab.spbu.ru/software/spades/
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.
Proper citation: SPAdes (RRID:SCR_000131) Copy
http://www.ccmb.med.umich.edu/ccdu/SNPAAMapper
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. A downstream variant annotation program that can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5?UTR, etc). Major features: * The pipeline accepts the VCF (Variant Call Format) input file in tab-delimited format and processes the vcf input file containing all cases (G5, lowFreq, and novel) * The variant mapping step has the option of letting users select whether they want to report the bp distance between each identified intron variant and its nearby exon * The pipeline can deal with VCF files called by different SAMTools versions (0.1.18 and older ones) and also offers flexibility in dealing with vcf input files generated using SAMTools with two or three samples * The spreadsheet result file contains full protein sequences for both ref and alt alleles, which makes it easier for downstream protein structure/function analysis tools to take
Proper citation: SNPAAMapper (RRID:SCR_002012) Copy
http://sourceforge.net/projects/skewer/
Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences.
Proper citation: skewer (RRID:SCR_001151) Copy
https://github.com/princelab/mspire-simulator
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.
Proper citation: Mspire-Simulator (RRID:SCR_001431) Copy
Software package of molecular simulation programs. It is distributed into AmberTools15 and Amber14. AmberTools15 is a software package which can carry out complete molecular dynamics simulations with either explicit water or generalized Born solvent models. It is distributed in source code format and must be compiled in order to be used. Amber14 builds on AmberTools15 by adding the pmemd program, which provides better performance on multiple CPUs and dramatic speed improvements on GPUs compared to sander (molecular dynamics). GPU info, manuals, and tutorials are available on the website.
Proper citation: Assisted Model Building with Energy Refinement (AMBER) (RRID:SCR_014230) Copy
https://github.com/MikkelSchubert/paleomix
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software toolkit for the processing of ancient and modern HTS data. PALEOMIX also aids in metagenomic analysis of the extracts from the HTS processing.
Proper citation: PALEOMIX (RRID:SCR_015057) Copy
https://github.com/kendomaniac/docker4seq
Software R package to execute next generation sequencing computing applications, e.g. reads mapping and counting, wrapped in docker containers.
Proper citation: docker4seq (RRID:SCR_017006) Copy
Web portal for the administration of Norwegian e-Infrastructure for Life Sciences. Enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their genomics scale data. NeLS is one of the packages of the ELIXIR.NO project.
Proper citation: NeLS (RRID:SCR_016301) Copy
https://www.ruhr-uni-bochum.de/mpc/software/ProCon/index.html.en
Java based conversion tool for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. Used to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories.
Proper citation: ProCon - PROteomics CONversion (RRID:SCR_016363) Copy
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