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  • 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 (870 words) - 17:17, 22 April 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
  • Halla
    ...er, Emma Schwager,Jason Lloyd-Price, George Weingart, Yo Sup Moon, Xochitl C. Morgan, Levi Waldron, Eric A. Franzosa, Curtis Huttenhower. High-sensitivi
    3 KB (367 words) - 13:57, 25 March 2022
  • Svtyper
    C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Mar
    3 KB (360 words) - 14:04, 3 October 2022
  • MEGAHIT
    [https://www.ncbi.nlm.nih.gov/pubmed/25609793 Li, D., Liu, C-M., Luo, R., Sadakane, K., and Lam, T-W., (2015) MEGAHIT: An ultra-fast sin
    3 KB (367 words) - 18:31, 18 August 2022
  • ViennaRNA
    The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and compar
    3 KB (396 words) - 19:08, 10 June 2022
  • SHEsisPlus
    [1] Neigenfind J1, Gyetvai G, Basekow R, Diehl S, Achenbach U, Gebhardt C, Selbig J, Kersten B.Haplotype inference from unphased SNP data in heterozy
    3 KB (344 words) - 15:04, 19 August 2022
  • FSL
    #M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. NeuroImage, 62:7 #M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data
    3 KB (365 words) - 16:47, 17 January 2023
  • VS Code Remote Development
    # Use ''''Ctrl-C'''' key combination to stop the <code>tunnel</code> process. ...on requesting 4 cores, 15GB of RAM, an A100 GPU for 1 hour: <code>'''srun -c 4 --mem 15gb -p gpu --gres gpu:a100:1 -t 60 --pty bash -i'''</code>
    7 KB (1,100 words) - 17:42, 5 March 2024
  • Csubst
    '''CSUBST''' is a tool for analyzing '''C'''ombinatorial '''SUBST'''itutions of codon sequences in phylogenetic trees
    3 KB (380 words) - 22:12, 26 July 2023
  • MCarts
    Zhang, C. †, Lee, K.-Y., Swanson, M.S., Darnell, R.B. † 2013. Prediction of clus
    3 KB (399 words) - 14:53, 14 December 2022
  • Open3d
    ...exposes a set of carefully selected data structures and algorithms in both C++ and Python. The backend is highly optimized and is set up for paralleliza
    3 KB (414 words) - 17:16, 7 July 2023
  • TRNAscan-Se
    ...orithm from A. Pavesi's group). It runs on any UNIX system with Perl and a C compiler installed.
    3 KB (389 words) - 20:53, 12 August 2022
  • Pygenometracks
    * Hi-C matrices (as triangle or squares)
    3 KB (375 words) - 20:54, 18 May 2023
  • Caper
    ...a dependency of the [https://github.com/ENCODE-DCC/hic-pipeline ENCODE Hi-C uniform processing pipeline]. Caper wraps Cromwell to run pipelines on mult
    3 KB (425 words) - 14:43, 11 October 2023
  • Managing Python environments and Jupyter kernels
    mamba install cudatoolkit=11.3 pytorch=1.12.1=gpu_cuda* -c pytorch <code>mamba install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch</code>
    9 KB (1,491 words) - 17:32, 22 April 2024
  • ITK-SNAP
    ...h, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee, and Guido Gerig. User-guided 3D active contour segmentation of anatom
    3 KB (397 words) - 19:23, 12 August 2022
  • Gblocks
    Gblocks is a computer program written in ANSI C language that eliminates
    3 KB (441 words) - 13:56, 13 June 2022
  • Julia
    ...written in Julia itself, also integrates mature, best-of-breed open source C and Fortran libraries for linear algebra, random number generation, signal
    3 KB (412 words) - 20:49, 21 October 2022
  • Artemis
    Carver T, Berriman M, Tivey A, Patel C, Böhme U et al.
    3 KB (378 words) - 14:53, 12 August 2022
  • MMseqs2
    ...sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software
    3 KB (413 words) - 20:22, 2 October 2023
  • VarSimLab
    Quit the server with CONTROL-C.
    3 KB (420 words) - 17:24, 22 August 2022
  • Uproc
    ...ge-scale sequence analysis and is now available in terms of an open source C library. UProC is up to three orders of magnitude faster than profile-based
    3 KB (418 words) - 20:53, 12 August 2022
  • Gem5
    gem5 is written primarily in C++ and python and most components are provided under a BSD style license. It
    3 KB (434 words) - 19:23, 10 June 2022
  • SAMStat
    SAMStat is an efficient C program to quickly display statistics of large sequence files from next gen
    3 KB (429 words) - 20:34, 12 August 2022
  • Chewiesnake
    Deneke C, Uelze L, Brendebach H, Tausch SH and Malorny B (2021)
    4 KB (457 words) - 15:02, 23 October 2023
  • ART
    ...r the simulation study of the 1000 Genomes Project . ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART
    3 KB (440 words) - 21:10, 6 December 2019
  • FAQ
    ...cProfile for python code, [[Nsight]] Compute for CUDA apps, or VTune for C/C++ + MPI code.
    7 KB (1,199 words) - 02:11, 17 April 2024
  • MP-EST
    ...rees by maximizing a pseudo-likelihood function. The program is written in C. The parallel version of the program can run independent searches (chains)
    4 KB (489 words) - 12:01, 19 August 2022
  • Reptile
    Reptile is a software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing
    3 KB (458 words) - 21:46, 21 August 2022
  • Ea-utils
    :: Similar to audy's stitch program, but in C, more efficient and supports some automatic benchmarking and tuning. It use
    4 KB (438 words) - 14:54, 15 August 2022
  • Lazypipe
    ...taxonomic profiling of NGS libraries has been developed as a collection of C++, Perl and R scripts.
    4 KB (507 words) - 16:54, 14 December 2022
  • PennCNV
    Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H, Bucan M, Maris JM, Wang K. Adjustment of
    4 KB (474 words) - 21:23, 6 December 2019
  • Fast-Plast
    Marçais, G. and C. Kingsford. 2011. A fast, lock-free approach for efficient parallel countin
    4 KB (487 words) - 21:20, 6 December 2019
  • Matlab
    ...mputing problems faster than traditional programming languages, such as C, C++, and Fortran. -rw-r--r-- 1 root root 2900 Apr 3 10:08 houdini_main.c
    9 KB (1,361 words) - 16:06, 28 November 2023
  • SLURM Commands
    sinfo -o %P,%D,%c,%X,%m,%f
    4 KB (574 words) - 15:30, 25 April 2024
  • GROMACS
    Hess, B., Kutzner, C., van der Spoel, D. and Lindahl, E.
    4 KB (556 words) - 19:16, 5 January 2023
  • SnpEff
    *<pre>java -Xmx2g -jar $HPC_SNPEFF_DIR/jar/snpEff.jar download -c $HPC_SNPEFF_CONF/snpEff.config -v athalianaTair10</pre>
    4 KB (562 words) - 15:19, 5 January 2023
  • Python
    ...load the environment module and run <code>pip list</code> or <code>python -c "help('modules')"</code> command before submitting a request for a new modu
    5 KB (670 words) - 19:42, 3 February 2023
  • MetaBCC-LR
    -c 25000 \
    6 KB (774 words) - 14:28, 15 December 2022
  • How To ResVault
    #* You can save data in the default C:\ drive, but it will be wiped out at the end of every session. Therefore, c
    6 KB (953 words) - 20:01, 18 July 2023
  • Sate
    * Liu, K., S. Raghavan, S. Nelesen, C. R. Linder, T. Warnow, 2009. "Rapid and accurate large scale coestimation o * Liu, K., T.J. Warnow, M.T. Holder, S. Nelesen, J. Yu, A. Stamatakis, and C.R. Linder. "SATé-II: Very Fast and Accurate Simultaneous Estimation of Mul
    7 KB (910 words) - 20:43, 21 December 2022
  • Multi-Threaded & Message Passing Job Scripts
    *<code>-c, --cpus-per-task=<ncpus></code>
    9 KB (1,347 words) - 19:05, 21 July 2023
  • Conda
    mamba install cudatoolkit=11.3 pytorch=1.12.1=gpu_cuda* -c pytorch
    16 KB (2,392 words) - 20:14, 16 April 2024
  • User:Manoj
    FC="mpif90 -c" \ FC="mpif90 -c" \
    75 KB (8,369 words) - 08:47, 25 July 2013

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