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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 (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

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