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• 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
• News:2021-08-04
  ...The shutdown is scheduled from Aug. 9th through Aug. 15th, after Summer B/C and before fall classes start. The system will be back to normal operation
  2 KB (374 words) - 16:47, 23 August 2022
• 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
• 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 (827 words) - 18:02, 27 June 2024
• 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

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