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• 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
• Grib api
  The ECMWF GRIB API is an application program interface accessible from C,
  2 KB (278 words) - 17:22, 15 August 2022
• FastSpar
  FastSpar is a c++ implementation of the SparCC algorithm published here: Friedman, J. & Alm
  2 KB (283 words) - 15:26, 15 August 2022
• AEGeAn
  ...ble programs as well as several data structures and modules callable via a C API.
  2 KB (287 words) - 16:31, 10 June 2022
• SNeP
  SNeP is a piece of software written in C++ that performs historical Effective Population Size (Ne) trajectories esti
  2 KB (278 words) - 16:23, 10 June 2022
• UDUNITS
  1) a C library for units of physical quantities.
  2 KB (279 words) - 17:17, 22 August 2022
• RMATS turbo
  rMATS turbo is the C/Cython version of rMATS (refer to http://rnaseq-mats.sourceforge.net). The
  2 KB (289 words) - 19:26, 2 June 2022
• Gflags
  The gflags package contains a C++ library that implements commandline flags processing. It includes built-i
  2 KB (291 words) - 17:07, 15 August 2022
• RMATS-turbo
  rMATS turbo is the C/Cython version of rMATS (refer
  2 KB (292 words) - 18:14, 8 March 2022
• CGAL
  and reliable geometric algorithms in the form of a C++ library.The Computational
  2 KB (293 words) - 15:32, 6 June 2022
• Gaussian GUI
  **<pre>gui start -e gv -c 1 -m 8 -t 4</pre>
  2 KB (341 words) - 19:17, 25 January 2023
• SQANTI3
  ...i.nlm.nih.gov/pmc/articles/PMC5848618/ Tardaguila M, de la Fuente L, Marti C, et al. SQANTI: extensive characterization of long-read transcript sequence
  2 KB (290 words) - 20:35, 27 May 2022
• CGATools
  ...plete Genomics data. The focus is to provide command line utilities, but a C++ API is available as well. The general areas of functionality include geno
  2 KB (291 words) - 13:26, 15 August 2022
• Blitz
  Blitz++ is a C++ class library for scientific computing which provides performance on par
  3 KB (303 words) - 21:19, 6 December 2019
• TRITONSERVER
  ...rver. For edge deployments, Triton is available as a shared library with a C API that allows the full functionality of Triton to be included directly in
  2 KB (298 words) - 20:06, 21 August 2022
• CFITSIO
  CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexibl
  2 KB (291 words) - 13:26, 15 August 2022
• Bgenix
  Bgenix is a reference implementation of the BGEN format, written in C++. The library can be used as the basis for BGEN support in other software,
  2 KB (291 words) - 12:52, 15 August 2022
• NCBI C++ Toolkit
  NCBI C++ Toolkit provides free, portable, public domain libraries with no restrict
  3 KB (306 words) - 14:25, 19 August 2022
• Autometa
  ..., J.; Miller, I.; Baxa, J.; Lopera, J.; Kerby, R. L.; Rey, F. E.; Kwan, J. C. Autometa: Automated extraction of microbial genomes from individual shotgu
  3 KB (300 words) - 21:19, 6 December 2019
• Package-GFE
  ...and genotype frequencies from nucleotide read quartets (read counts of A, C, G, and T) derived from individual high-throughput sequencing data for mult
  2 KB (280 words) - 16:45, 10 June 2022
• Mono
  ...plementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime. A growing family of solutions and an acti
  2 KB (289 words) - 17:41, 15 August 2022
• Sputnik
  Sputnik is a C language program that searches dna sequence files in Fasta format for micro
  2 KB (311 words) - 15:50, 22 August 2022
• PhiSpy
  PhiSpy is a computer program written in C++, Python and R to identify prophages in a complete bacterial genome sequen
  2 KB (291 words) - 21:23, 6 December 2019
• BloomTree
  C++ and is open source.
  3 KB (302 words) - 16:49, 10 June 2022
• Bamtools
  BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM
  2 KB (289 words) - 18:02, 12 August 2022
• NAMD
  James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Eliza
  2 KB (245 words) - 13:45, 19 August 2022
• PRINSEQ++
  Chan chan PRINSEQ++ is a C++ implementation of the prinseq-lite.pl program. It can be used to filter,
  2 KB (298 words) - 18:11, 15 April 2020
• SURVIVOR
  [https://www.nature.com/articles/ncomms14061 Jeffares, Daniel C; Jolly, Clemency; Hoti, Mimoza; Speed, Doug; Shaw, Liam; Rallis, Charalampo
  3 KB (296 words) - 21:24, 6 December 2019
• MSMBuilder
  ...ls (MSMs). It is primarily written in the python programming language with C extensions for the most time consuming routines. MSMs are a powerful means
  2 KB (288 words) - 16:38, 10 June 2022
• Mega2
  Baron RV, Kollar C, Mukhopadhyay N, Weeks DE (2014) Mega2: validated data-reformatting for lin
  3 KB (310 words) - 21:21, 6 December 2019
• MPFR
  The MPFR library is a C library for multiple-precision floating-point computations with correct rou
  2 KB (302 words) - 21:22, 6 December 2019
• Mlpack
  Written in C++ and built on the Armadillo linear algebra library, the ensmallen numerica
  3 KB (301 words) - 19:43, 15 December 2020
• MetaCompare
  [https://www.ncbi.nlm.nih.gov/pubmed/29718191 Oh, M., Pruden, A., Chen, C., Heath, L. S., Xia, K., & Zhang, L. (2018). MetaCompare: A computational p
  3 KB (304 words) - 21:21, 6 December 2019
• PHYUTILITY
  Smith, S. A. and Dunn, C. W. (2008) Phyutility: a phyloinformatics tool for trees, alignments, and m
  2 KB (296 words) - 20:22, 12 August 2022
• FEniCS
  ...models into efficient finite element code. With the high-level Python and C++ interfaces to FEniCS, it is easy to get started, but FEniCS offers also p
  3 KB (301 words) - 21:20, 6 December 2019
• Isonclust2
  isONclust2 is implemented in C++, which makes it fast enough to cluster large transcriptomic datasets prod
  3 KB (303 words) - 15:23, 28 October 2022
• Mitsuba2
  Mitsuba 2 is a research-oriented rendering system written in portable C++17. It consists of a small set of core libraries and a wide variety of plu
  3 KB (302 words) - 20:45, 18 August 2022
• MIGRATE-N
  ...ult to use? In G. Bertorelle, M. W. Bruford, H. C. Hauffe, A. Rizzoli, and C. Vernesi, editors, Population Genetics for Animal Conservation, volume 17 o
  5 KB (636 words) - 16:05, 22 December 2022
• Gaussian
  ...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.
  6 KB (918 words) - 14:39, 8 March 2023
• Metaxa2
  ...1/1755-0998.12399/abstract Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2: Improved Identification and T
  3 KB (300 words) - 19:29, 18 August 2022
• LZO
  LZO is a portable lossless data compression library written in ANSI C.
  3 KB (317 words) - 20:38, 10 June 2022
• Bigslice
  ...' (or '''B'''iosynthetic '''G'''ene clusters - '''S'''uper '''Li'''near '''C'''lustering '''E'''ngine) is a tool designed to cluster massive numbers of
  3 KB (295 words) - 21:25, 14 September 2023
• ADMB
  AD Model Builder, or ADMB, is a C++ application which implements AD using specialized classes and operator ov
  3 KB (302 words) - 20:49, 11 August 2022
• ATLAS
  software. The current version provides a complete BLAS API (for both C and
  3 KB (317 words) - 15:19, 12 August 2022
• PHAST
  ...reconstruction of ancestral sequences. It consists of over 60,000 lines of C code.
  3 KB (320 words) - 17:17, 10 June 2022
• DecontaMiner
  ...aMiner must be present in your configure.txt file (which is passed by the -c option when you run decontaMiner.sh). In order to use the pre-loaded tools
  3 KB (321 words) - 14:56, 2 March 2021
• TRUST4
  ...solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 (CDR
  3 KB (314 words) - 20:12, 8 February 2021
• SSH Multiplexing
  ControlPath ~/.ssh/control/%C
  2 KB (342 words) - 13:40, 26 June 2023
• P4est
  ...est.github.io/papers/BursteddeWilcoxGhattas11.pdf Carsten Burstedde, Lucas C. Wilcox, and Omar Ghattas, p4est: Scalable Algorithms for Parallel Adaptive
  3 KB (320 words) - 17:24, 10 June 2022
• VeryFastTree
  ...formatics/article/36/17/4658/5861530 César Piñeiro, José M. Abuín and Juan C. Pichel. Bioinformatics, vol. 36, no. 17, pages 4658-4659, 2020.]
  3 KB (329 words) - 21:03, 12 February 2021
• Bamm
  ...ology 2014, and Evolution 2015). BAMM is a command line program written in C++. Post-run analysis and visualization is performed using the R package BAM
  3 KB (322 words) - 18:00, 12 August 2022
• MRtrix
  ...felt, R. Tabbara, T. Dhollander, M. Pietsch, D. Christiaens, B. Jeurissen, C.-H. Yeh, and A. Connelly. MRtrix3: A fast, flexible and open software frame
  3 KB (311 words) - 20:34, 24 August 2022
• GPU Access
  ...dia CUDA Toolkit]] page. The current CUDA environment is cuda/11. However, C++ or Python packages numba and PyCuda are other ways to program GPU algorit mamba install cudatoolkit=11.3 pytorch=1.12.1=gpu_cuda* -c pytorch
  5 KB (767 words) - 20:15, 16 April 2024
• Emerald
  emeraLD v0.1 (c) 2018 corbin quick (corbinq@gmail.com)
  3 KB (324 words) - 19:16, 29 October 2023
• Silo
  compile $(CC) -c yourfile.c and link with $(CLINKER) -o yourprog
  3 KB (356 words) - 17:28, 10 June 2022
• REMORA
  [http://dl.acm.org/citation.cfm?id=2834999 C. Rosales, A. Gómez-Iglesias, A. Predoehl. "REMORA: a Resource Monitoring T
  3 KB (330 words) - 20:39, 24 August 2022
• Gawk
  ...e discarding the rest. To write a program to do this in a language such as C or Pascal is a time-consuming inconvenience that may take many lines of cod
  3 KB (356 words) - 16:55, 15 August 2022
• IsoSel
  ...id=10.1371/journal.pone.0174250 Philippon H., Souvane A., Brochier-Armanet C. and Perrière, G. (2017) IsoSel: Protein Isoform Selector for Phylogenetic
  3 KB (345 words) - 14:29, 26 March 2021
• TGICL
  launch_tgicl tgicl -F sample.fasta -q sample.qual -c 4
  3 KB (340 words) - 20:47, 12 August 2022
• Finesse
  Finesse is written in C and is compiled into a single binary executable called 'kat'. Today the pre
  3 KB (347 words) - 00:01, 9 July 2020
• Talon
  ...hua Zeng, Brian Williams, Diane Trout, Whitney England, Sophie Chu, Robert C. Spitale, Andrea J. Tenner, Barbara J. Wold, Ali Mortazavi bioRxiv 672931;
  3 KB (321 words) - 15:13, 23 September 2022
• SNPhylo
  Lee, T. H., Guo, H., Wang, X., Kim, C., & Paterson, A. H. (2014). SNPhylo: a pipeline to construct a phylogenetic
  3 KB (340 words) - 17:48, 10 June 2022
• ElPrep
  .../journals.plos.org/plosone/article?id=10.1371/journal.pone.0209523 Herzeel C, Costanza P, Decap D, Fostier J, Verachtert W (2019) elPrep 4: A multithrea
  3 KB (345 words) - 21:20, 6 December 2019
• SpliceGrapher
  * M. F. Rogers, C. Boucher, A. Ben-Hur. SpliceGrapherXT: from splice graphs to transcripts us
  3 KB (318 words) - 21:24, 6 December 2019
• GeNomad
  ...chal Babinski, Yan Xu, Bin Hu, Patrick S. G. Chain, Stephen Nayfach, Nikos C. Kyrpides bioRxiv 2023.03.05.531206; doi: https://doi.org/10.1101/2023.03.0
  3 KB (332 words) - 13:25, 7 April 2023
• MGLTools
  components implemented in Python and C++ (With Python bindings).
  3 KB (357 words) - 17:03, 6 June 2022
• DeepGS
  ...5-018-2976-9 Ma, W., Qiu, Z., Song, J., Li, J., Cheng, Q., Zhai, J., & Ma, C. (2018). A deep convolutional neural network approach for predicting phenot
  3 KB (342 words) - 22:21, 26 August 2020
• Hiphase
  [https://doi.org/10.1093/bioinformatics/btae042 Holt, J. M., Saunders, C. T., Rowell, W. J., Kronenberg, Z., Wenger, A. M., & Eberle, M. (2024). HiP
  3 KB (337 words) - 20:21, 19 March 2024
• 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
  6 KB (873 words) - 18:15, 18 January 2024
• Probalign
  ...CH benchmarks. Probalign improvements are largest on datasets containing N/C terminal extensions and on datasets with long and heterogeneous length sequ
  3 KB (349 words) - 19:36, 21 August 2022
• Uropa
  Kondili M, Fust A, Preussner J, Kuenne C, Braun T, and Looso M. UROPA: a tool for Universal RObust Peak Annotation.
  3 KB (337 words) - 15:42, 6 September 2022
• Imoka
  Lorenzi, C., Barriere, S., Villemin, J. et al. iMOKA: k-mer based software to analyze
  3 KB (346 words) - 17:07, 27 May 2022
• SNP-sites
  ...making it feasible to run on modest computers. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.
  3 KB (334 words) - 12:56, 15 August 2022
• SEQuel
  sequel -c sample.fasta -ap reads_aln.sam -i 404
  3 KB (382 words) - 22:39, 21 August 2022
• Numba
  ...ing NumPy arrays. Other, less well-typed code will be translated to Python C-API calls effectively removing the "interpreter" but not removing the dynam
  3 KB (353 words) - 20:44, 15 August 2022
• HybPiper
  ...dner, E. M., Liu, Y., Medina, R., Goffinet, B., Shaw, A. J., Zerega, N. J. C, and Wickett, N. J. (2016). HybPiper: Extracting Coding Sequence and Intron
  3 KB (349 words) - 18:36, 10 June 2022
• UCSC
  ...much more. Library subroutines are available for everything from managing C data structures such as linked lists, balanced trees, hashes, and directed
  3 KB (349 words) - 20:53, 12 August 2022
• Nipype
  Gorgolewski K, Burns CD, Madison C, Clark D, Halchenko YO, Waskom ML, Ghosh SS. (2011). Nipype: a flexible, li
  3 KB (348 words) - 20:07, 12 August 2022
• Sdsl
  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) - 17:47, 15 August 2022
• Theano
  * dynamic C code generation – Evaluate expressions faster.
  3 KB (345 words) - 15:58, 6 June 2022
• Humann2
  ...gart G, Schwarzberg Lipson K, Knight R, Caporaso JG, Segata N, Huttenhower C. Species-level functional profiling of metagenomes and metatranscriptomes.
  3 KB (348 words) - 22:26, 27 August 2020
• Aquamis
  Deneke, C.; Brendebach, H.; Uelze, L.; Borowiak, M.; Malorny, B.; Tausch, S.H.
  3 KB (348 words) - 22:07, 20 October 2023
• R Benchmark 2.5
  | Linear regr. over a 3000x3000 matrix (c = a \ b') || 12.57 || 5.92 || 1.37 || 0.41
  2 KB (216 words) - 20:33, 15 August 2022
• CONSEL
  CONSEL is a program package consists of small programs written in C language. It calculates the probability value (i.e., p-value) to assess the
  3 KB (375 words) - 18:43, 10 June 2022
• ALLMAPS
  ...biomedcentral.com/articles/10.1186/s13059-014-0573-1 Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable J, Schnable P, Lyons E, Lu J. (2015) ALLMAPS: ro
  3 KB (361 words) - 21:11, 6 December 2019
• NeEstimator
  ...rary_effective_population_size_Ne_from_genetic_data_Mol_Ecol_Resour_14 Do, C., Waples, R. S., Peel, D., Macbeth, G. M., Tillett, B. J. & Ovenden, J. R.
  3 KB (375 words) - 19:56, 12 August 2022
• ANGSD
  ...specially useful for low and medium depth data. The software is written in C++ and has been used on large sample sizes.
  3 KB (355 words) - 12:42, 12 August 2022
• IOAPI
  ...mming library for data storage and access, available from both Fortran and C. The same routines can be used for both file storage (using netCDF files) a
  2 KB (341 words) - 19:35, 24 August 2022
• Using SSH Keys To Access HPG
  **<pre>ssh-keygen -o -a 100 -t ed25519 -f ~/.ssh/id_ed25519 -C "Comment to make the key recognizable among many"</pre> **<pre>ssh-keygen -t ed25519 -C "Comment to make the key recognizable among many"</pre>
  6 KB (1,087 words) - 18:54, 29 March 2024
• ResFinder
  ...Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM. Journal of Antimicrobial Chemotherapy. 2020 Aug 11.
  3 KB (342 words) - 18:41, 23 April 2021
• VTK
  ...D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk,
  3 KB (360 words) - 20:55, 12 August 2022
• VirusDetect
  ...rect.com/science/article/pii/S0042682216303166 Zheng Y, Gao S, Padmanabhan C, Li R, Galvez M, Gutierrez D, Fuentes S, Ling K-S, Kreuze J, Fei Z (2017) V
  3 KB (377 words) - 23:22, 30 July 2020
• ROOTPy
  ...interacting with ROOT in Python should not feel like you are still writing C++.
  3 KB (389 words) - 16:49, 21 August 2022
• FALCON
  ...for haploid and diploid genomes. It has some back-end code implemented in C for speed and some simple front-end written in Python for convenience.
  3 KB (395 words) - 15:19, 15 August 2022
• Cowast
  ...rs MPI enabled. At HiperGator we use OPENMPI. In addition, matching netcdf-c, netcdf-f and HDF5 modules must be present.
  3 KB (443 words) - 13:28, 27 March 2024
• Anchorwave
  ...tiago Marco-Sola, Miquel Moreto, Lynn Johnson, Edward S. Buckler, Michelle C. Stitzer. AnchorWave: Sensitive alignment of genomes with high sequence div
  3 KB (367 words) - 21:10, 20 September 2023
• Plasme
  $ PLASMe.py test.fasta test.plasme.fna -c 0.6 -i 0.6 -p 0.5 -t 8
  3 KB (375 words) - 18:08, 3 April 2024
• Metacrast
  ...hed work, please include a reference to my PeerJ article: Moller AG, Liang C. (2017) MetaCRAST: reference-guided extraction of CRISPR spacers from unass
  3 KB (392 words) - 17:58, 27 May 2022
• Xander
  ...rticles/10.1186/s40168-015-0093-6 Wang, Q., J. A. Fish, M. Gilman, Y. Sun, C. T. Brown, J. M. Tiedje and J. R. Cole. Xander: Employing a Novel Method fo
  3 KB (381 words) - 19:07, 10 June 2022
• AFNI
  AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) da
  3 KB (363 words) - 20:52, 11 August 2022

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