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https://github.com/FePhyFoFum/phyx
Software phylogenetic tools for unix. Used to perform phylogenetics analyses on trees and sequences. Collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects.
Proper citation: Phyx (RRID:SCR_024164) Copy
https://qtltools.github.io/qtltools/
Software tool set for molecular Quantitative Trait Loci discovery and analysis. Allows to go from raw sequence data to collection of molecular Quantitative Trait Loci in few easy-to-perform steps.
Proper citation: qtltools (RRID:SCR_024200) Copy
Open source software for image computation with main focus on high performance volumetric registration, segmentation, and image processing of volumetric medical images.
Proper citation: Plastimatch (RRID:SCR_024168) Copy
Software command line utility and library for lossy compression of PNG images. The conversion reduces file sizes significantly and preserves full alpha transparency. Generated images are compatible with all web browsers and operating systems.
Proper citation: pngquant (RRID:SCR_024169) Copy
https://github.com/ggonnella/rgfa
Ruby library for handling GFA files.
Proper citation: rgfa (RRID:SCR_024323) Copy
https://gitlab.com/RKIBioinformaticsPipelines/QCumber
Software for quality control, quality trimming, adapter removal and sequence content check of NGS data.
Proper citation: qcumber (RRID:SCR_024203) Copy
https://github.com/scottgigante/picopore
Software tool for reducing the storage size of Oxford Nanopore Technologies datasets without loss of functionality.
Proper citation: picopore (RRID:SCR_024161) Copy
Platform independent JAVA software for analysis of sequence based typing methods that generate allelic profiles and their associated epidemiological data.Phylogenetic inference and data visualization for sequence based typing methods.
Proper citation: PHYLOViZ (RRID:SCR_024162) Copy
Open Source software modular Java libraries for cheminformatics.
Proper citation: CDK (RRID:SCR_023985) Copy
https://github.com/gramos/imagetooth
Software library to generate images for odontograms.Allows to choose between png or jpg images.
Proper citation: ImageTooth (RRID:SCR_024039) Copy
https://github.com/rdpstaff/TaxonomyTree
Software library used by other RDP tools.TaxonomyTree building and traversal utility classes.
Proper citation: TaxonomyTree (RRID:SCR_024090) Copy
https://metacpan.org/dist/Sort-Key-Top
Functions available from this module select the top n elements from a list using several common orderings and custom key extraction procedures.
Proper citation: Sort-Key-Top (RRID:SCR_024092) Copy
https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen
Software library as set of classes for creating statistical genetic programs.
Proper citation: libStatGen (RRID:SCR_024093) Copy
https://github.com/rvaser/thread_pool
Software C++ thread pool library.
Proper citation: ThreadPool (RRID:SCR_024094) Copy
https://opencfu.sourceforge.net/
Software to count cell colonies and other circular objects. Used to facilitate enumeration of colony forming unit.
Proper citation: OpenCFU (RRID:SCR_024142) Copy
https://github.com/rizkg/BBHash
Software library for building minimal perfect hash function. Designed to handle large scale datasets.
Proper citation: BBHash (RRID:SCR_023972) Copy
Software DICOM library which provides user-friendly C++11 and Python API for different parts of the DICOM standard.
Proper citation: Odil (RRID:SCR_024140) Copy
https://github.com/jdidion/atropos
Software tool for specific, sensitive, and speedy trimming of NGS reads.
Proper citation: Atropos (RRID:SCR_023962) Copy
Software Python library for phylogenetic computing. Provides classes and functions for simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: DendroPy (RRID:SCR_024197) Copy
https://github.com/y-256/libdivsufsort
Software library that implements lightweight suffix array construction algorithm. Provides C API to construct suffix array and Burrows-Wheeler transformed string from given string over constant size alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1) bytes of memory space, where n is the length of the string.
Proper citation: libdivsufsort (RRID:SCR_024079) Copy
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