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  • Compilers
    ...n-us/intel-parallel-studio-xe Intel Compiler Suite] provides Fortran and C/C++ compilers and is preferred compiler option on hipergator. The [https://gcc.gnu.org GNU Compiler Suite] provides Fortran and C/C++ compilers.
    1 KB (159 words) - 22:30, 26 July 2021
  • Intel MPI
    mpicc ( C source) mpiCC (C++ source)
    3 KB (291 words) - 21:21, 6 December 2019
  • SWIG
    [[Category:Software]][[Category:library]][[Category:development]][[Category:C++]][[Category:python]] ...the 'glue code' required for the above target languages to call into the C/C++ code. SWIG can also export its parse tree in the form of XML and Lisp s-e
    3 KB (416 words) - 21:24, 6 December 2019
  • Swig
    ...the 'glue code' required for the above target languages to call into the C/C++ code. SWIG can also export its parse tree in the form of XML and Lisp s-e
    3 KB (400 words) - 21:29, 6 December 2019
  • HiC-Pro
    ...ng dilution Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C, capture Hi-C or HiChip data. ..., Heard E., Barillot E. HiC-Pro: An optimized and flexible pipeline for Hi-C processing. Genome Biology 2015, 16:259 doi:10.1186/s13059-015-0831-x
    3 KB (426 words) - 16:41, 28 June 2021
  • Boost
    "Boost provides free peer-reviewed portable C++ source libraries. We emphasize libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and u
    3 KB (346 words) - 21:05, 6 December 2019
  • Amber Job Sample Scripts
    sander -O -i amber.in -o amber.log -p amber.prmtop -c amber.inpcrd mpiexec sander.MPI -O -i amber.in -o amber.log -p amber.prmtop -c amber.inpcrd
    1 KB (167 words) - 17:38, 26 June 2017
  • Xerces
    |{{#vardefine:url|http://xerces.apache.org/#xerces-c}} ...or parsing, generating, manipulating, and validating XML documents. Xerces-C++ is faithful to the XML 1.0 and 1.1 recommendations and many associated st
    3 KB (306 words) - 21:29, 6 December 2019
  • LDhat
    ...n rates from population genetic data. The package is available either as C/C++ source code.
    3 KB (294 words) - 21:21, 6 December 2019
  • CryptoMiniSat
    ...ython interface provides a high-level yet efficient API to use most of the C++ interface with ease.
    3 KB (324 words) - 21:00, 6 December 2019
  • Juicer
    ...stq raw data files and command line tools for feature annotation on the Hi-C maps.
    2 KB (275 words) - 21:22, 6 December 2019
  • GNU Compiler Collection
    The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go, as well as libraries for these languages (libs
    3 KB (300 words) - 21:20, 6 December 2019
  • Doxygen
    annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba and
    3 KB (399 words) - 21:20, 6 December 2019
  • Intel Compilers
    Intel® Cluster Studio features the acclaimed Intel Fortran and C++ Compilers. These performance-oriented compilers can deliver a remarkable Intel Compilers support OpenMP. Developers using C or C++ can create and manage portable, shared-memory parallelism in their applic
    3 KB (327 words) - 21:21, 6 December 2019
  • ProtExcluder
    ...e, G. D., Hunagel, D. E., Lei, J., Achawanantakun, R., Jiao, D., Lawrence, C. J., Ware, D., Shiu, S-H., Childs, K. L., Sun, Y., Jiang, N, Yandell, M. 20
    3 KB (329 words) - 21:22, 6 December 2019
  • Intel Compilers and Libraries
    | C || icc || ''icc compiler_options example.c'' | C++ || icpc || ''icpc compiler_options -o example.exe example.cxx''
    5 KB (656 words) - 16:48, 13 November 2017
  • Dlib
    ...ing machine learning algorithms and tools for creating complex software in C++ to solve real world problems. See http://dlib.net for the main project do
    2 KB (269 words) - 13:11, 4 May 2020
  • Armadillo
    Armadillo is a high quality C++ linear algebra library, aiming towards a good balance between speed and e ...://arma.sourceforge.net/armadillo_nicta_2010.pdf Armadillo: An Open Source C++ Linear Algebra Library for Fast Prototyping and Computationally Intensive
    2 KB (263 words) - 21:19, 6 December 2019
  • SALSA
    A tool to scaffold long read assemblies with Hi-C Ghurye, J., Pop, M., Koren, S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assemblies using long range contact in
    2 KB (266 words) - 21:24, 6 December 2019
  • VSCode
    ...s and has a rich ecosystem of extensions for other languages (such as C++, C#, Java, Python, PHP, Go) and runtimes (such as .NET and Unity).
    2 KB (287 words) - 21:29, 6 December 2019
  • NetCDF
    ...e that the Fortran module man not have all supporting binaries that netcdf-c module has.
    3 KB (379 words) - 20:27, 2 August 2021
  • HiCAssembler
    Hi-C scaffolding tool to assemble contigs/scaffolds into complete chromosomes ...Valsecchi, Sarah Toscano, Laura Arrigoni, Fidel Ramirez, Asifa Akhtar. "Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes
    2 KB (282 words) - 14:23, 21 October 2020
  • SUNDIALS
    ...marsh, P. N. Brown, K. E. Grant, S. L. Lee, R. Serban, D. E. Shumaker, and C. S. Woodward, "SUNDIALS: Suite of Nonlinear and Differential/Algebraic Equa * R. Serban and A. C. Hindmarsh, "CVODES: the Sensitivity-Enabled ODE Solver in SUNDIALS," Proce
    3 KB (356 words) - 21:31, 6 December 2019
  • GRACKLE
    ...ry for astrophysical simulations and models. Grackle has interfaces for C, C++, Fortran, and Python codes and provides:
    2 KB (290 words) - 22:15, 27 August 2020
  • GSL
    The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General
    2 KB (280 words) - 21:31, 6 December 2019
  • BERTopic
    BERTopic is a topic modeling technique that leverages transformers and c-TF-IDF to create dense clusters allowing for easily interpretable topics wh [https://zenodo.org/record/4719700 BERTopic: Leveraging BERT and c-TF-IDF to create easily interpretable topics.]
    2 KB (282 words) - 17:35, 25 May 2021
  • HOOMD
    J. A. Anderson, C. D. Lorenz, and A. Travesset. General purpose molecular dynamics simulation ...D. Nguyen, J. A. Anderson, P. Liu, F. Spiga, J. A. Millan, D. C. Morse, S. C. Glotzer. Strong scaling of general-purpose molecular dynamics simulations
    5 KB (603 words) - 21:21, 6 December 2019
  • ImageMagick
    ...re (C), MagickWand (C), ChMagick (Ch), ImageMagickObject (COM+), Magick++ (C++), JMagick (Java), L-Magick (Lisp), Lua, NMagick (Neko/haXe), Magick.NET (
    3 KB (375 words) - 21:22, 6 December 2019
  • Plinkseq
    PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus
    2 KB (296 words) - 21:22, 6 December 2019
  • VCFLib
    vcflib is a simple C++ library for parsing and manipulating VCF files. This library provides a simple API to map each VCF record into a C++ class. See included applications for example usage.
    2 KB (285 words) - 21:29, 6 December 2019
  • OpenCV
    ...des several hundreds of computer vision algorithms. Written in optimized C/C++, the library can take advantage of multi-core processing. Enabled with Op
    2 KB (283 words) - 21:31, 6 December 2019
  • PLINKSEQ
    PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus
    2 KB (288 words) - 21:22, 6 December 2019
  • GEOS
    ...te (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the ​OpenGIS Simple Features for SQL spatial predica
    3 KB (306 words) - 04:31, 24 March 2021
  • Tuning Analysis Utilities
    ...olkit for performance analysis of parallel programs written in Fortran, C, C++, UPC, Java, Python. ...methods, basic blocks, and statements as well as event-based sampling. All C++ language features are supported including templates and namespaces. The A
    4 KB (445 words) - 21:29, 6 December 2019
  • DCMTK
    ...orage and worklist servers. DCMTK is is written in a mixture of ANSI C and C++. It comes in complete source code and is made available as "open source"
    3 KB (299 words) - 21:21, 6 December 2019
  • GDSL
    ...ary fully written from scratch in pure ANSI C. It is designed to offer for C programmers common data structures with powerful algorithms, and hidden imp
    3 KB (305 words) - 22:06, 27 August 2020
  • TAU
    ...olkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python. ...h instrumentation of functions, methods, basic blocks, and statements. All C++ language features are supported including templates and namespaces. The A
    4 KB (575 words) - 21:31, 6 December 2019
  • LAMMPS
    ...liquid, solid, or gaseous state. It is a open source software, written in C++ and developed at Sandia laboratory. It can be used to model atomic, polym ...CMAKE_INSTALL_PREFIX=<target_lammps_dir> -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake ../cmake
    3 KB (467 words) - 23:34, 20 August 2021
  • Segemehl
    Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermueller J: "F Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt L, Teupser D, H
    3 KB (404 words) - 21:24, 6 December 2019
  • KIM
    * C * C++
    3 KB (323 words) - 21:21, 6 December 2019
  • OpenCL
    ...evelopers can launch compute kernels written using a limited subset of the C programming language on a GPU. ...wget -q https://raw.github.com/smistad/OpenCL-Getting-Started/master/main.c
    3 KB (358 words) - 21:22, 6 December 2019
  • SHARCGS
    Dohm JC, Lottaz C, Borodina T, Himmelbauer H SHARCGS, a fast and highly accurate short-read a Dohm JC, Lottaz C, Borodina T, Himmelbauer H Substantial biases in ultra-short read data sets
    3 KB (314 words) - 21:24, 6 December 2019
  • 3d-dna
    ...n: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017. ...A.P., et al. (2017). De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science eaal3327. Published online ahea
    3 KB (326 words) - 21:10, 6 December 2019
  • PICRUSt
    ...le, D. E.; Vega Thurber, R. L.; Knight, R.; Beiko, R. G.; and Huttenhower, C. Nature Biotechnology, 1-10. 8 2013.]
    3 KB (342 words) - 21:22, 6 December 2019
  • Sdsl
    [[Category:Software]][[Category:library]][[Category:c++]] The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. In total, the library co
    3 KB (350 words) - 21:24, 6 December 2019
  • Maq
    maqindex -i -c consensus.cns all.map; maqview -c consensus.cns all.map
    3 KB (367 words) - 21:21, 6 December 2019
  • Minimac
    ...rnals.org/content/early/2014/10/22/bioinformatics.btu704.short Fuchsberger C, Abecasis GR, Hinds DA. minimac2: faster genotype imputation. Bioinformatic Howie B, Fuchsberger C, Stephens M, Marchini J, and Abecasis GR. Fast and accurate genotype imputa
    3 KB (332 words) - 21:22, 6 December 2019
  • HOMER
    ...many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.
    3 KB (325 words) - 21:21, 6 December 2019
  • Biolite
    BioLite is a bioinformatics framework written in Python/C++ that automates the collection and reporting of diagnostics, tracks proven * A C++ library 'seqio' for efficient I/O of large NGS data files
    3 KB (363 words) - 21:20, 6 December 2019
  • Phenix
    .... Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010).
    3 KB (320 words) - 21:22, 6 December 2019
  • Elastix
    ...Elastix, making it available in languages like C++, Python, Java, R, Ruby, C# and Lua.
    3 KB (366 words) - 13:41, 6 April 2020
  • Edta
    ...J., Lugo C. S. B., Elliott T. A., Ware D., Peterson T., Jiang N.✉, Hirsch C. N.✉ and Hufford M. B.✉ (2019). Benchmarking Transposable Element Annot
    3 KB (357 words) - 22:32, 26 August 2020
  • CUDA Examples
    ===cuda_bm.c=== {{#fileAnchor: cuda_bm.c}}
    11 KB (1,462 words) - 20:33, 21 June 2017
  • BUCKy
    [http://mbe.oxfordjournals.org/content/24/2/412.abstract?etoc C. Ané, B. Larget, D.A. Baum, S.D. Smith, A. Rokas (2007). Bayesian estimati ...l.pdf?ijkey=BIwQBlPEqeEiojQ&keytype=ref B. Larget, S.K. Kotha, C.N. Dewey, C. Ané (2010). BUCKy: Gene tree / species tree reconciliation with the Bayes
    3 KB (384 words) - 21:06, 6 December 2019
  • Mamba
    Mamba is a reimplementation of the conda package manager in C++. core parts of mamba are implemented in C++ for maximum efficiency
    3 KB (432 words) - 15:06, 19 July 2021
  • Tensorboard
    ...orBoard 2.4.0 at '''<nowiki>http://localhost:6006/</nowiki>''' (Press CTRL-C to quit)
    1 KB (184 words) - 18:18, 20 January 2022
  • Usearch
    Edgar, Robert C. - Search and clustering orders of magnitude faster than BLAST Author : Edgar, Robert C.
    4 KB (535 words) - 21:29, 6 December 2019
  • ChartDirector
    VBScript, VBA, JavaScript, .NET (C#/VB), Java, JSP, C++, PHP, Perl, Python,
    3 KB (392 words) - 21:17, 6 December 2019
  • PICSL
    [1] H. Wang, J. W. Suh, S. Das, J. Pluta, C. Craige, P. Yushkevich, "Multi-atlas segmentation [2] H. Wang, S. R. Das, J. W. Suh, M. Altinay, J. Pluta, C. Craige, B. B. Avants, and P. A. Yushkevich,
    3 KB (394 words) - 16:48, 25 October 2021
  • Xpra Windows Installation
    "/drives/c/Program Files/Xpra/Xpra" "$@"
    2 KB (300 words) - 17:27, 30 July 2019
  • Using SSH Keys To Access HPG
    ssh-keygen -o -a 100 -t ed25519 -f ~/.ssh/id_ed25519 -C "Comment to make the key recognizable among many" ssh-keygen -o -a 100 -t ed25519 -f ~/.ssh/id_ed25519 -C "Comment to make the key recognizable among many"
    3 KB (563 words) - 14:30, 14 May 2021
  • CASM
    [ref2] J. C. Thomas, A. Van der Ven, Finite-temperature properties of strongly anharmon [ref4] A. Van der Ven, J. C. Thomas, Q. Xu, J. Bhattacharya “Linking the electronic structure of soli
    4 KB (452 words) - 21:11, 6 December 2019
  • MolPro
    ...ckert, E. Goll, C. Hampel, A. Hesselmann, G. Hetzer, T. Hrenar, G. Jansen, C. Köppl, Y. Liu, A. W. Lloyd, R. A. Mata, A. J. May, S. J. McNicholas, W. M
    3 KB (472 words) - 21:22, 6 December 2019
  • AMBER
    ...Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. The Amber biomolecular simulation progra ...-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (20
    5 KB (758 words) - 21:16, 6 December 2019
  • NAMD
    James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Eliza
    2 KB (249 words) - 17:04, 6 September 2017
  • FFTW
    Fastest Fourier Transform in the West, is a C library for computing the Discrete Fourier Transform (DFT) in one or more d
    2 KB (219 words) - 20:27, 2 August 2021
  • Persistent Terminal Sessions
    ...eate as many terminal windows in the screen session as needed with 'Ctrl+a c' key combination. See [[Screen]] documentation. Ctrl+a c
    4 KB (701 words) - 15:51, 9 July 2020
  • Vcf-validator
    Validation suite for Variant Call Format (VCF) files, implemented using C++11
    2 KB (247 words) - 21:29, 6 December 2019
  • CellProfiler
    ...arch Computing. To run CellProfiler in batch mode, you should include the -c or --run-headless option. Also, you want to use CELLPROFILER_USE_XVFB="1" -c, --run-headless Run headless (without the GUI)
    7 KB (869 words) - 21:12, 6 December 2019
  • AI Help
    ...loped by Facebook AI Research Lab and has interfaces for Python, Java, and C++, but is most commonly used with Python. It supports training on both GPU ...-GPU and distributed training. APIs are available for Python, Java, Go and C++. See our [[TensorFlow|TensorFlow quickstart page]] for help getting start
    4 KB (607 words) - 00:34, 26 October 2021
  • OpenSim
    SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.
    2 KB (247 words) - 17:47, 22 September 2021
  • OpenSlide
    OpenSlide is a C library that provides a simple interface to read whole-slide images
    2 KB (248 words) - 21:22, 6 December 2019
  • Tbb
    Widely used C++ template library for task parallelism.
    2 KB (259 words) - 21:29, 6 December 2019
  • Talesf
    TALESF is a C library for identifying potential binding sites for transcription activator
    2 KB (256 words) - 21:29, 6 December 2019
  • Fastp
    ...e fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
    2 KB (254 words) - 21:20, 6 December 2019
  • Mach2VCF
    Mach2VCF is a C++ tool to convert MaCH files to VCF files.
    2 KB (242 words) - 21:22, 6 December 2019
  • Unanimity
    C++ library and its applications to generate and process accurate consensus s
    2 KB (266 words) - 21:29, 6 December 2019
  • Glog
    C++ implementation of the Google logging module
    2 KB (269 words) - 21:21, 6 December 2019
  • LEMON
    Networks. It is a C++ template library providing efficient implementations
    2 KB (266 words) - 21:21, 6 December 2019
  • DosageConvertor
    DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther format
    2 KB (254 words) - 21:21, 6 December 2019
  • NEXUS NCL
    The Nexus Class Library (NCL) is a C++ library for interpreting data files created according to the NEXUS file f
    2 KB (253 words) - 21:22, 6 December 2019
  • Torch
    ..., thanks to an easy and fast scripting language, LuaJIT, and an underlying C/CUDA implementation.
    2 KB (251 words) - 21:29, 6 December 2019
  • Mpi4py
    ...1/2/3 specification and exposes an API which grounds on the standard MPI-2 C++ bindings.
    2 KB (268 words) - 21:22, 6 December 2019
  • IGoR
    IGoR is a C++ software designed to infer V(D)J recombination related processes from seq
    2 KB (271 words) - 13:52, 14 May 2020
  • Eagle-rc
    ...s.biomedcentral.com/articles/10.1186/s12920-018-0342-1 Tony Kuo and Martin C Frith and Jun Sese and Paul Horton. EAGLE: Explicit Alternative Genome Like
    2 KB (270 words) - 22:30, 26 August 2020
  • MetaSV
    ...oup.com/bioinformatics/article/31/16/2741/321286 Marghoob Mohiyuddin, John C. Mu, Jian Li, Narges Bani Asadi, Mark B. Gerstein, Alexej Abyzov, Wing H. W
    2 KB (277 words) - 21:21, 6 December 2019
  • IMa2p
    IMa2p is a parallel implementation of IMa2, using OpenMPI-C++ - a Bayesian MCMC based method for inferring population demography under
    2 KB (277 words) - 21:21, 6 December 2019
  • QT
    QT is a cross-platform application and UI framework for developers using C++ or QML, a CSS & JavaScript like language.
    2 KB (250 words) - 21:31, 6 December 2019
  • Phylonet
    C. Than, D. Ruths, L. Nakhleh (2008) PhyloNet: A software package for analyzi
    2 KB (263 words) - 21:23, 6 December 2019
  • Grib api
    The ECMWF GRIB API is an application program interface accessible from C,
    2 KB (274 words) - 21:21, 6 December 2019
  • Nexus Class Library (NCL)
    The Nexus Class Library (NCL) is a C++ library for interpreting data files created according to the NEXUS file f
    2 KB (283 words) - 21:23, 6 December 2019
  • MiRanda
    ...finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. MiRanda was develo
    2 KB (278 words) - 21:21, 6 December 2019
  • NetCDF-C
    |{{#vardefine:app|netcdf-c}}
    2 KB (279 words) - 04:31, 24 March 2021
  • Ghmm
    The General Hidden Markov Model library (GHMM) is a freely available C library implementing efficient data structures and algorithms for basic and
    2 KB (285 words) - 21:20, 6 December 2019
  • Rust
    ...both functional and imperative paradigms. Rust is syntactically similar to C++, but its designers intend it to provide better memory safety while still
    2 KB (285 words) - 21:24, 6 December 2019
  • GenomeTools
    ...nome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.
    2 KB (266 words) - 21:21, 6 December 2019
  • Libunistring
    ...t provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
    2 KB (267 words) - 21:21, 6 December 2019
  • Gaussian
    gui start -e gv -c 1 -m 8 -t 4 ...aramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G.
    7 KB (1,030 words) - 20:52, 20 January 2022
  • TomoPy
    Gursoy D, De Carlo F, Xiao X and Jacobsen, C. (2014). J. Synchrotron Rad. 21, doi:10.1107/S1600577514013939
    2 KB (276 words) - 21:29, 6 December 2019
  • Capnp
    [[Category:Software]][[Category:C++]]
    2 KB (288 words) - 21:01, 6 December 2019

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