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https://sourceforge.net/projects/poamsa/
Software application for multiple sequence alignment in bioinformatics. Has superior ability to handle branching / indels in the alignment.
Proper citation: POA (RRID:SCR_024172) Copy
https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index
Software application as protein�ligand interaction profiler to identify non-covalent interactions between biological macromolecules and their ligands. Provides atom level information on binding characteristics as well as publication ready visualizations and parsable output files. PLIP web tool is based on PLIP command line tool and offers graphical interface for analysis of few structures.
Proper citation: PLIP (RRID:SCR_024173) Copy
https://github.com/Washington-University/CiftiLib
Software C++ Library for reading and writing CIFTI-2 and CIFTI-1 files.
Proper citation: CiftiLib (RRID:SCR_023996) Copy
https://github.com/COMBINE-lab/RapMap
Software tool for mapping RNA-seq reads to transcriptomes. Used for rapid sensitive and accurate read mapping via quasi-mapping
Proper citation: rapmap (RRID:SCR_024204) Copy
https://github.com/rvaser/bioparser/
Software C++ library for parsing several formats in bioinformatics. C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.
Proper citation: Bioparser (RRID:SCR_024065) Copy
https://github.com/silx-kit/pyFAI
Open source Python software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments.
Proper citation: pyFAI (RRID:SCR_024186) Copy
Software memory efficient bioinformatics library written in D programming language whose aim is to provide platform for developing high performance computational biology applications using the D programming language through automatic parallelization of tasks where possible and by avoiding unnecessary memory allocations.
Proper citation: BioD (RRID:SCR_024062) Copy
https://github.com/IRCAD-IHU/camp
Software multi-purpose reflection library developped by Technogerma Systems France and then by Tegesoft. Provides extra layer of flexibility to programs, and allows them to fully expose their data structures at runtime.
Proper citation: CAMP (RRID:SCR_023981) Copy
https://github.com/rvalieris/parallel-fastq-dump
Software wrapper to speed up downloading process by dividing the work into multiple threads.
Proper citation: parallel-fastq-dump (RRID:SCR_024150) Copy
https://github.com/ggonnella/gfapy
Software library for handling sequence graphs in Python.
Proper citation: GfaPy (RRID:SCR_024030) Copy
Software application as simultaneous Bayesian inference of alignment and phylogeny. Used to estimate multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. to explore the joint space of alignment and phylogeny given molecular sequence data. BAli-Phy version 3 is model based co-estimation of alignment and phylogeny. Version 3 is substantially faster for large trees, and implements covarion models, additional codon models and other new models. Implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously.
Proper citation: BAli-Phy (RRID:SCR_023976) Copy
https://github.com/FlorianThibord/OptimiR
Software miRSeq data alignment workflow. Used to integrate genetic information to assess the impact of variants on miRNA expression. Used for integrating genome wide genotype data into miRNA sequence alignment analysis.
Proper citation: OptimiR (RRID:SCR_024149) Copy
https://ismrmrd.github.io/apidocs/1.5.0/
Prerequisite for sharing magnetic resonance imaging reconstruction algorithms and code is a common raw data format. This repository describes such common raw data format, which attempts to capture the data fields that are required to describe the magnetic resonance experiment with enough detail to reconstruct images. The repository also contains a C/C++ library for working with the format.
Proper citation: ISMRMRD (RRID:SCR_024043) Copy
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
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