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Category:Software
Or you can browse through the sub-categories or software package names in the table below. To add a documentation page for a new piece of software installed into /apps please go to [[Add New App Page]].

2,137 members (62 subcategories, 0 files) - 19:53, 20 February 2024
Installed Software

26 bytes (2 words) - 17:41, 28 September 2017
Software Development
#REDIRECT [[Software Development Policies]]

43 bytes (4 words) - 20:46, 6 June 2022
Software Development Policies
==External Software Components== ...d to get a security review or risk assessment for such software. Only when software is exposed to the outside world, e.g. as part of PubApps, will a security r

533 bytes (84 words) - 15:43, 19 August 2022

Page text matches

FLEA
[[Category:Software]][[Category:Phylogenetics]]

2 KB (260 words) - 22:01, 27 August 2020
Detectron2
[[Category:Software]][[Category:Library]]

3 KB (295 words) - 19:33, 15 July 2021
Xesmf
[[Category:Software]][[Category:Math]][[Category:Climate]]

2 KB (248 words) - 20:05, 24 August 2022
Unrar
[[Category:Software]][[Category:utility]]

2 KB (239 words) - 19:16, 3 June 2022
Recycler
[[Category:Software]]

3 KB (297 words) - 14:21, 11 October 2022
Coevol
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

3 KB (399 words) - 18:37, 12 August 2022
Category:Statistics
[[Category:Math]][[Category:Software]] Statistical software

16 members (0 subcategories, 0 files) - 15:29, 23 August 2022
GROCSVs
[[Category:Software]][[Category:Phylogenetics]] Genome-wide Reconstruction of Complex Structural Variants, or GROC-SVs, is a software pipeline for identifying large-scale structural variants, performing sequen

2 KB (274 words) - 21:21, 6 December 2019
Meta-Tissue
[[Category:Software]][[Category:Biology]][[Category:Genomics]] Meta-Tissue is a free software for identifying eQTLs from multiple tissues. It uses meta-analysis to combi

3 KB (328 words) - 19:24, 18 August 2022
Kneaddata
[[Category:Software]][[Category:Phylogenetics]]

3 KB (324 words) - 14:36, 4 September 2020
GenomeThreader
[[Category:Software]][[Category:phylogenetics]] GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions

3 KB (315 words) - 16:35, 29 November 2021
CellRanger
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]] |{{#vardefine:url|https://support.10xgenomics.com/single-cell/software/pipelines/latest/what-is-cell-ranger}}

2 KB (294 words) - 18:24, 12 August 2022
ProbABEL
[[Category:Software]][[Category:Genomics]][[Category:Biology]] ProbABEL software package is used for the analysis of genome-wide imputed SNP data and quanti

3 KB (371 words) - 19:35, 21 August 2022
Tombo
[[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]]

2 KB (247 words) - 19:28, 1 June 2022
Clann
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] It is also important for the user to know that the software is designed to

3 KB (438 words) - 18:30, 12 August 2022
BEDTools
[[Category:Software]][[Category:Biology]][[Category:NGS]] |{{#vardefine:exe|}} 

3 KB (485 words) - 12:48, 15 August 2022
Evigene
[[Category:Software]][[Category:Phylogenetics]] ...methods involve using available best-of-breed gene prediction and assembly software, combining all evidence for genes, from expressed sequences, genome assembl

3 KB (372 words) - 21:21, 6 December 2019
ViennaRNA
[[Category:Software]][[Category:Biology]][[Category:RNA-Seq]]

3 KB (396 words) - 19:08, 10 June 2022
Mlstcheck
[[Category:Software]][[Category:Phylogenetics]] ...ndrew J. Page, Ben Taylor, Jacqueline A. Keane, The Journal of Open Source Software, (2016).]

3 KB (395 words) - 18:06, 27 May 2022
Faqcs
[[Category:Software]][[Category:Genomics]][[Category:Biology]]

2 KB (268 words) - 17:48, 18 May 2023
ArrayFire
[[Category:Software]][[Category:Math]]

3 KB (315 words) - 14:52, 12 August 2022
PDA
[[Category:Software]][[Category:biology]][[Category:phylogenetics]] |{{#vardefine:url|http://www.cibiv.at/software/pda/}}

3 KB (294 words) - 21:23, 6 December 2019
NGC CLI
[[Category:Software]][[Category:shell]]

2 KB (282 words) - 16:25, 19 August 2022
SpinalCordToolbox
[[Category:Software]][[Category:Phylogenetics]]

2 KB (253 words) - 18:43, 1 June 2022
Rnalysis
[[Category:Software]] RNAlysis is a Python-based software for analyzing RNA sequencing data. RNAlysis allows you to build customized

5 KB (648 words) - 16:12, 25 April 2023
Category:Linux
[[Category:Infrastructure]][[Category:Software]]

7 members (0 subcategories, 0 files) - 15:17, 12 July 2012
PhyloBayes
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] |{{#vardefine:exe|}} 

3 KB (375 words) - 20:20, 12 August 2022
Bayenv
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

3 KB (388 words) - 19:03, 10 June 2022
Giraf
[[Category:Software]] |{{#vardefine:url|http://www.cs.cmu.edu/~ckingsf/software/giraf/}}

3 KB (382 words) - 21:12, 7 December 2022
Ldak
[[Category:Software]][[Category:Phylogenetics]][[Category:Biology]] LDAK is a software package for analysing association study data.

2 KB (265 words) - 19:48, 15 August 2022
NCBI C++ Toolkit
[[Category:Software]][[Category:Biology]][[Category:programming]][[Category:library]][[Category

3 KB (306 words) - 14:25, 19 August 2022
BioBakery
[[Category:Software]][[Category:Phylogenetics]]

2 KB (285 words) - 14:04, 3 February 2022
SQLite
[[Category:Software]][[Category:Database]]

3 KB (339 words) - 13:32, 13 June 2022
Category:Mapping
[[Category:Software]]

8 members (0 subcategories, 0 files) - 17:22, 3 June 2022
Molden
[[Category:Software]][[Category:Chemistry]][[Category:Structure]] |{{#vardefine:exe|1}} 

2 KB (255 words) - 14:14, 5 October 2023
QT
[[Category:Software]][[Category:Library]] |{{#vardefine:exe|}} 

2 KB (257 words) - 20:57, 21 August 2022
Satsuma2
[[Category:Software]][[Category:Phylogenetics]]

2 KB (243 words) - 18:10, 1 June 2022
Circompara2
[[Category:Software]][[Category:Phylogenetics]]

2 KB (283 words) - 21:36, 1 April 2022
LTRRetriever
[[Category:Software]][[Category:biology]][[Category:phylogenetics]]

2 KB (255 words) - 21:21, 6 December 2019
NLR-Parser
[[Category:Software]][[Category:Phylogenetics]]

3 KB (318 words) - 20:07, 21 April 2020
QUIP
[[Category:Software]][[Category:Phylogenetics]] ...and is also able to call external packages, and serve as plugins to other software such as LAMMPS, CP2K and also the python framework ASE. Various hybrid comb

3 KB (315 words) - 21:02, 21 August 2022
AStalavista
[[Category:Software]][[Category:Biology]][[Category:Genomics]]

2 KB (284 words) - 14:56, 12 August 2022
Cogent
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

2 KB (294 words) - 21:06, 6 December 2019
Gaussian galaxy-input
[[Category:Galaxy]][[Category:Software]]

261 bytes (40 words) - 14:24, 30 June 2017
ASE-ANI
[[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]]

2 KB (303 words) - 14:55, 12 August 2022
VASP
[[Category:Software]][[Category:Chemistry]] |{{#vardefine:exe|}} 

4 KB (550 words) - 19:00, 21 July 2023
Iaps
[[Category:Software]]

2 KB (250 words) - 18:42, 8 February 2023
Stumpy
[[Category:Software]][[Category:Workflow Automation]] ...calable Python Library for Time Series Data Mining. Journal of Open Source Software, 4(39), 1504.

3 KB (430 words) - 15:16, 13 April 2023
Albacore
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

2 KB (258 words) - 21:10, 6 December 2019
RAiSD
[[Category:Software]][[Category:Phylogenetics]] RAiSD (Raised Accuracy in Sweep Detection) is a stand-alone software implementation of the μ statistic for selective sweep detection. Unlike ex

2 KB (292 words) - 17:38, 14 July 2020
Minigraph
[[Category:Software]][[Category:Phylogenetics]]

2 KB (279 words) - 18:08, 31 March 2021
Megraft
[[Category:Software]][[Category:Biology]][[Category:Sequencing]] |{{#vardefine:url|http://microbiology.se/software/megraft/}}

3 KB (293 words) - 18:35, 18 August 2022
Numba
[[Category:Software]][[Category:Compiler]]

3 KB (353 words) - 20:44, 15 August 2022
GMcloser
[[Category:Software]][[Category:Biology]][[Category:NGS]]

3 KB (321 words) - 17:25, 10 June 2022
DynamicDBG
[[Category:Software]][[Category:Phylogenetics]] ...membership queries for de Bruijn graphs was recently proposed in [1]. This software is an implementation of the data structure in [1] with dynamic edges (and n

3 KB (312 words) - 21:20, 6 December 2019
STAR-CCM+
[[Category:Software]][[Category:Fluid Dynamics]] |{{#vardefine:exe|1}} 

3 KB (363 words) - 16:01, 22 August 2022
FrameDP
[[Category:Software]][[Category:Biology]][[Category:Sequencing]]

2 KB (249 words) - 15:07, 10 June 2022
FSA
[[Category:Software]][[Category:Phylogenetics]]

3 KB (307 words) - 20:38, 23 May 2022
Vray
[[Category:Software]] |{{#vardefine:url|https://www.chaos.com/3d-rendering-software}}

3 KB (341 words) - 16:46, 6 April 2023
Chipyard
[[Category:Software]][[Category:Simulation]] ...FPGA-accelerated simulation (FireSim), automated VLSI flows (Hammer), and software workload generation for bare-metal and Linux-based systems (FireMarshal). C

3 KB (360 words) - 14:30, 11 October 2022
GFam
[[Category:Software]]

3 KB (339 words) - 17:06, 15 August 2022
OCaml
[[Category:Software]][[Category:Language]][[Category:Programming]]

2 KB (240 words) - 17:27, 19 August 2022
Gcnenv
[[Category:Software]][[Category:Math]]

2 KB (243 words) - 19:38, 20 June 2023
LongStitch
[[Category:Software]] [[Category:Genomics]] [[Category:Biology]]

3 KB (314 words) - 19:00, 10 October 2022
Fastp
[[Category:Software]][[Category:Biology]][[Category:NGS]]

2 KB (256 words) - 15:23, 15 August 2022
CLHEP
[[Category:Software]][[Category:Physics]] |{{#vardefine:exe|}} 

2 KB (309 words) - 14:10, 13 June 2022
Tiff
[[Category:Software]][[Category:Imaging]] This software provides support for the Tag Image File Format (TIFF), a widely used format

2 KB (246 words) - 19:19, 1 June 2022
Relernn
[[Category:Software]]

2 KB (261 words) - 21:20, 6 February 2024
ARKS
[[Category:Software]][[Category:Phylogenetics]]

2 KB (285 words) - 21:15, 6 December 2019
Fastx Toolkit
[[Category:Software]][[Category:Biology]][[Category:NGS]] |{{#vardefine:exe|}} 

2 KB (257 words) - 16:37, 15 August 2022
RFAA
[[Category:Software]][[Category:Biology]][[Category:Genomics]] ...abases and structure templates as well as required dependencies to run the software. However, users should download the contents of the repo locally to run the

3 KB (323 words) - 16:56, 27 March 2024
Starseqr
[[Category:Software]][[Category:Phylogenetics]]

2 KB (269 words) - 17:12, 31 May 2022
Illumina-utils
[[Category:Software]][[Category:Phylogenetics]]

2 KB (295 words) - 18:43, 15 August 2022
Gotcloud
[[Category:Software]][[Category:Phylogenetics]]

2 KB (244 words) - 22:14, 27 August 2020
ParlAI
[[Category:Software]][[Category:Phylogenetics]] title={ParlAI: A Dialog Research Software Platform},

3 KB (301 words) - 15:55, 21 July 2021
WOMBAT
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

3 KB (325 words) - 21:29, 6 December 2019
Breakseq
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

2 KB (247 words) - 21:15, 6 December 2019
Hacdivsel
[[Category:Software]][[Category:Genomics]][[Category:Biology]]

2 KB (280 words) - 22:20, 10 October 2022
IGTP
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] Oliver Eulenstein, "iGTP: A software package for large-scale gene tree

3 KB (318 words) - 19:06, 12 August 2022
Bamtools
[[Category:Software]][[Category:NGS]][[Category:Biology]][[Category:Sequencing]] |{{#vardefine:exe|}} 

2 KB (289 words) - 18:02, 12 August 2022
GTDBTk
[[Category:Software]][[Category:Phylogenetics]] GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and

3 KB (299 words) - 15:08, 12 April 2022
FFTW
[[Category:Software]][[Category:Library]][[Category:Compiler]][[Category:Math]]

2 KB (223 words) - 16:41, 15 August 2022
KLayout
[[Category:Software]][[Category:Phylogenetics]]

2 KB (257 words) - 19:33, 15 August 2022
Nextclade
[[Category:Software]]

2 KB (260 words) - 19:03, 12 January 2023
ORCA
[[Category:Software]][[Category:Chemistry]][[Category:Structure]]

3 KB (399 words) - 14:03, 2 April 2024
ESOM
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

2 KB (242 words) - 15:08, 15 August 2022
DiscoVista
[[Category:Software]][[Category:Phylogenetics]] DiscoVista (Discordance Visualization Tool) is a command-line software package for visualizing phylogenetic discordance. The package is written by

3 KB (291 words) - 19:00, 28 January 2020
OpenPose
[[Category:Software]][[Category:Programming]][[Category:Library]]

4 KB (497 words) - 18:44, 30 January 2023
BamUtil
[[Category:Software]][[Category:Biology]][[Category:Genomics]]

3 KB (328 words) - 18:02, 12 August 2022
Tensorboard
...separate workload within a HiPerGator Desktop session. Many neural network software frameworks are able to stream training data to a TensorBoard log file.

2 KB (231 words) - 21:03, 12 December 2023
MGEfinder
[[Category:Software]][[Category:Phylogenetics]]

2 KB (254 words) - 13:55, 14 September 2020
Comp-D MPI
[[Category:Software]][[Category:Statistics]]

2 KB (264 words) - 16:54, 9 June 2022
NONMEM
[[Category:Software]][[Category:Modeling]]

3 KB (439 words) - 21:23, 6 December 2019
SNPTEST
[[Category:Software]][[Category:Phylogenetics]] ...is designed to work seamlessly with the output of our genotype imputation software IMPUTE [1] and the programs QCTOOL and GTOOL. This program was used in the

3 KB (302 words) - 16:17, 2 January 2020
P4vasp
[[Category:Software]][[Category:Visualization]]

2 KB (230 words) - 18:01, 19 August 2022
GenGen
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] GenGen is a suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The

3 KB (326 words) - 17:36, 10 June 2022
PALES
[[Category:Software]][[Category:Physics]] |{{#vardefine:url|http://spin.niddk.nih.gov/bax/software/PALES/index.html}}

3 KB (355 words) - 18:06, 19 August 2022
GSNP
[[Category:Software]][[Category:Biology]][[Category:NGS]] |{{#vardefine:url|http://jil.genomics.org.cn/index.php/en/software/gsnp.html}}

3 KB (459 words) - 17:27, 15 August 2022
CMWP
[[Category:Software]][[Category:Biology]][[Category:Genomics]]

3 KB (329 words) - 17:57, 10 June 2022
Lima
[[Category:Software]][[Category:Phylogenetics]]

3 KB (299 words) - 19:57, 15 August 2022
Skmer
[[Category:Software]][[Category:genomics‏‎]][[Category:Biology]]

2 KB (260 words) - 13:31, 15 August 2022
MicrobeAnnotator
[[Category:Software]][[Category:Annotation]][[Category:Biology]]

2 KB (270 words) - 19:02, 10 October 2022
ONT-Bonito
[[Category:Software]][[Category:Phylogenetics]]

2 KB (242 words) - 14:40, 25 February 2020
GeneSeqer
[[Category:Software]][[Category:Biology]][[Category:Genomics]]

2 KB (257 words) - 18:58, 12 August 2022
Xterm
[[Category:Software]][[Category:Shell]]

2 KB (278 words) - 19:37, 11 July 2022
NAMD
[[Category:Software]][[Category:Molecular Dynamics]]

2 KB (245 words) - 13:45, 19 August 2022
Pandoc
[[Category:Software]][[Category:Utility]]

3 KB (300 words) - 16:31, 21 August 2022
MinkowskiEngine
[[Category:Software]][[Category:Machine Learning]]

2 KB (256 words) - 17:52, 31 May 2022
AutoDock-GPU
[[Category:Software]][[Category:Chemistry]]

3 KB (332 words) - 15:25, 12 August 2022
MEGA
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] Software suite for analyzing DNA and protein sequence data from species and populati

3 KB (337 words) - 20:30, 15 December 2020
Run dbcan
[[Category:Software]][[Category:Biology]]

3 KB (377 words) - 16:48, 9 June 2023
Mapclassify
[[Category:Software]]

3 KB (314 words) - 18:21, 18 August 2022
GTAHunter
[[Category:Software]][[Category:Phylogenetics]]

3 KB (317 words) - 16:39, 27 May 2022
MiXCR
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] MiXCR is a universal software for fast and accurate analysis of raw T- or B- cell receptor repertoire seq

3 KB (340 words) - 21:22, 6 December 2019
MetaVelvet
[[Category:Software]][[Category:genomics]][[Category:Biology]]

3 KB (326 words) - 19:28, 18 August 2022
Biodiverse
[[Category:Software]][[Category:Phylogenetics]]

3 KB (329 words) - 21:03, 6 December 2019
Category:Python
[[Category:Software]]

3 members (0 subcategories, 0 files) - 21:56, 1 February 2014
SNPGenie
[[Category:Software]][[Category:Phylogenetics]]

3 KB (423 words) - 18:41, 1 June 2022
Zstd
[[Category:Software]][[Category:Phylogenetics]]

2 KB (264 words) - 17:55, 22 August 2022
CLIFinder
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

3 KB (308 words) - 21:11, 6 December 2019
Guppy
[[Category:Software]][[Category:Phylogenetics]]

4 KB (506 words) - 21:07, 14 December 2022
BayesTraits
[[Category:Software]][[Category:Phylogenetics]]

3 KB (329 words) - 17:49, 26 August 2022
Trinotate
[[Category:Software]][[Category:Biology]] Additional software included in this module:

3 KB (344 words) - 20:29, 7 December 2023
Uproc
[[Category:Software]][[Category:Genomics]][[Category:Biology]]

3 KB (418 words) - 20:53, 12 August 2022
RnaQUAST
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]][[Category:RNA-

2 KB (257 words) - 21:57, 21 August 2022
DeepLabCut
[[Category:Software]][[Category:Phylogenetics]]

3 KB (385 words) - 21:20, 6 December 2019
DAKOTA
[[Category:Software]][[Category:Math]] |{{#vardefine:exe|}} 

4 KB (484 words) - 18:26, 14 December 2022
Nsight
[[Category:Software]][[Category:Utility]][[Category:GPU]][[Category:Performance Analysis]]

3 KB (316 words) - 20:39, 24 August 2022
Pathoscope
[[Category:Software]][[Category:Sequencing]][[Category:Genomics]][[Category:Biology]]

3 KB (323 words) - 17:02, 21 August 2022
Filtlong
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

2 KB (299 words) - 21:20, 6 December 2019
CDNA Cupcake
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]]

2 KB (276 words) - 13:24, 15 August 2022
Nemo
[[Category:Software]][[Category:Machine Learning]]

2 KB (290 words) - 17:58, 15 August 2022
AEGeAn
[[Category:Software]][[Category:Biology]][[Category:Genomics]]

2 KB (287 words) - 16:31, 10 June 2022
Seq crumbs
[[Category:Software]][[Category:biology]][[Category:sequencing]][[Category:genomics]][[Category ...th Unix pipes to create complex pipelines. There are already other similar software that uses this approach like fastx and biopieces.

3 KB (328 words) - 15:12, 27 May 2022
TreeShrink
[[Category:Software]][[Category:Phylogenetics]]

2 KB (251 words) - 21:29, 6 December 2019
MRIcron
[[Category:Software]][[Category:Biology]][[Category:Imaging]]

3 KB (329 words) - 20:33, 24 August 2022
Msfinder
[[Category:Software]][[Category:Biology]][[Category:Chemistry]] ...omputational MS/MS fragmentation and structure elucidation using MS-FINDER software. Analytical Chemistry 88, 7946-7958, 2016.]

3 KB (290 words) - 13:32, 19 August 2022
Firefox
[[Category:Software]][[Category:Linux]]

3 KB (318 words) - 16:28, 19 October 2022
BLAT
[[Category:Software]][[Category:Biology]][[Category:Genomics]] |{{#vardefine:exe|1}} 

3 KB (484 words) - 13:03, 15 August 2022
CRISPRCasFinder
[[Category:Software]][[Category:Phylogenetics]]

2 KB (288 words) - 21:11, 6 December 2019
ADMB
[[Category:Software]][[Category:Math]][[Category:Modeling]]

3 KB (302 words) - 20:49, 11 August 2022
IsoSeq3
[[Category:Software]][[Category:Biology]][[Category:NGS]]

3 KB (295 words) - 20:10, 24 August 2022
Hal
[[Category:Software]][[Category:Phylogenetics]]

3 KB (366 words) - 18:11, 15 August 2022
BinSanity
[[Category:Software]][[Category:Biology]][[Category:Genomics]]

3 KB (288 words) - 16:54, 10 June 2022
Bzip2
[[Category:Software]][[Category:Utility]][[Category:Library]]

2 KB (289 words) - 13:16, 15 August 2022
Ont fast5 api
[[Category:Software]][[Category:Phylogenetics]] Oxford Nanopore Technologies fast5 API software

2 KB (238 words) - 17:49, 19 August 2022
EMMAX
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Mapping]]

3 KB (304 words) - 15:06, 15 August 2022
Mosaic
[[Category:Software]][[Category:Phylogenetics]]

2 KB (282 words) - 14:15, 14 October 2021
LoFreq
[[Category:Software]][[Category:Phylogenetics]]

2 KB (244 words) - 21:21, 6 December 2019
Python
[[Category:Software]][[Category:Language]][[Category:Programming]] |{{#vardefine:exe|1}} 

5 KB (670 words) - 19:42, 3 February 2023
Nuke
[[Category:Software]]

2 KB (277 words) - 13:47, 19 July 2023
SLAW
[[Category:Software]][[Category:Chemistry]][[Category:Spectroscopy]]

3 KB (389 words) - 23:49, 21 August 2022
IGV
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Phylogenetics]] |{{#vardefine:url|http://software.broadinstitute.org/software/igv/}}

2 KB (276 words) - 18:42, 15 August 2022
Pascal
[[Category:Software]][[Category:Compiler]][[Category:Programming]]

3 KB (303 words) - 20:44, 15 August 2022
Cammiq
[[Category:Software]][[Category:Biology]][[Category:Genomics]] CAMMiQ is a software tool for microbial identification and quantification.

2 KB (281 words) - 21:39, 14 June 2023
Automlsa2
[[Category:Software]]

2 KB (266 words) - 15:25, 12 August 2022
Bismark
[[Category:Software]][[Category:Biology]][[Category:NGS]]

2 KB (293 words) - 18:17, 12 August 2022
Pbsmrtpipe
[[Category:Software]][[Category:Biology]][[Category:Programming]]

2 KB (239 words) - 18:05, 15 August 2022
Badread
[[Category:Software]][[Category:Phylogenetics]] ...RR. Badread: simulation of error-prone long reads. Journal of Open Source Software. 2019;4(36):1316. doi:10.21105/joss.01316.]

3 KB (363 words) - 20:47, 24 September 2020
Plotsr
[[Category:Software]]

2 KB (271 words) - 20:00, 5 August 2022
Ghostscript
[[Category:Software]][[Category:Documentation]]

2 KB (254 words) - 17:08, 15 August 2022
EggNOG-mapper
[[Category:Software]][[Category:Phylogenetics]]

3 KB (364 words) - 19:29, 6 December 2021
GraphMap2
[[Category:Software]][[Category:Phylogenetics]]

2 KB (240 words) - 19:06, 21 July 2022
Regtools
[[Category:Software]][[Category:Biology]][[Category:RNA-Seq]][[Category:Genomics]]

2 KB (254 words) - 21:41, 21 August 2022
DIYABC
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] '''Note:''' this software is installed, but not supported as the upstream authors do not consider it

2 KB (300 words) - 14:41, 15 August 2022
QD
[[Category:Software]][[Category: Library]][[Category: Math]][[Category:Compiler]]

2 KB (271 words) - 17:47, 15 August 2022
Basemount
[[Category:Software]][[Category:Biology]][[Category:Sequencing]]

3 KB (375 words) - 18:50, 10 June 2022
Nonpareil
[[Category:Software]][[Category:Phylogenetics]]

2 KB (269 words) - 15:48, 17 November 2020
Fslmrs
[[Category:Software]][[Category:Spectroscopy]][[Category:Chemistry]] ...ingle voxel and multi-voxel (MRSI) datasets. FSL-MRS is part of FSL (FMRIB Software Library).

3 KB (293 words) - 16:50, 15 August 2022
IPOPT
[[Category:Software]][[Category:Library]][[Category:Math]][[Category:Compiler]] Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization.

2 KB (263 words) - 17:46, 15 August 2022
Open-cravat
[[Category:Software]] Please see: Open-CRAVAT Docs for installation instructions and software documentation.

3 KB (388 words) - 20:12, 12 August 2022
Wgd
[[Category:Software]][[Category:Phylogenetics]]

2 KB (270 words) - 19:52, 27 May 2022
Freesasa
[[Category:Software]][[Category:biology]][[Category:Molecular Dynamics]]

2 KB (276 words) - 16:49, 15 August 2022
Trgt
[[Category:Software]]

2 KB (273 words) - 14:45, 28 July 2023
GSL
[[Category:Software]][[Category:Library]][[Category:Data Science]] |{{#vardefine:url|http://www.gnu.org/software/gsl}}

2 KB (300 words) - 17:27, 15 August 2022
Grf
[[Category:Software]][[Category:biology]][[Category:Genomics]]

2 KB (278 words) - 17:21, 15 August 2022
Valgrind
[[Category:Software]][[Category:Programming]] |{{#vardefine:exe|}} 

2 KB (275 words) - 21:31, 6 December 2019
LFMM
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

3 KB (337 words) - 19:50, 15 August 2022
Lrgapcloser
[[Category:Software]][[Category:Biology]]

3 KB (326 words) - 19:30, 12 August 2022
MetaGeneMark
[[Category:Software]][[Category:Biology]][[Category:Genomics]]

2 KB (298 words) - 21:22, 6 December 2019
KrakenUniq
[[Category:Software]][[Category:Phylogenetics]]

3 KB (350 words) - 19:35, 15 August 2022
Whiteboxtools
[[Category:Software]][[Category:Phylogenetics]] ...it is meant to serve as an analytical backend for other data visualization software, mainly GIS.

3 KB (408 words) - 17:43, 22 August 2022
POV-Ray
[[Category:Software]] ...uter graphics. POV-Ray is Free Software (as per the definition of the Free Software Foundation) as its source code is licensed under the Affero General Public

2 KB (269 words) - 19:17, 27 May 2022
Category:Material Science
[[Category:Software]]

5 members (0 subcategories, 0 files) - 19:53, 22 August 2022
TAU
[[Category:Software]][[Category:library]][[Category:Performance Analysis]] |{{#vardefine:exe|}} 

4 KB (581 words) - 22:37, 24 October 2022
Plasflow
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

2 KB (292 words) - 20:17, 31 May 2022
Wannier90
[[Category:Software]][[Category:Physics]] |{{#vardefine:exe|}} 

2 KB (268 words) - 21:31, 6 December 2019
Localbrainage
[[Category:Software]][[Category:Biology]][[Category:Machine Learning]]

2 KB (238 words) - 19:30, 12 August 2022
CGView
[[Category:Software]][[Category:Phylogenetics]]

3 KB (351 words) - 19:39, 23 May 2022
TreeBreaker
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

2 KB (271 words) - 21:29, 6 December 2019
BDG-SeQuila
[[Category:Software]][[Category:Phylogenetics]]

3 KB (323 words) - 21:41, 26 August 2020
ProtHint
[[Category:Software]]

3 KB (329 words) - 20:27, 12 August 2022
CNVkit
[[Category:Software]][[Category:Phylogenetics]]

2 KB (254 words) - 13:50, 15 August 2022
Test
[[Category:Software]][[Category:shell]]

2 KB (229 words) - 21:29, 6 December 2019
Imagej2
[[Category:Software]]

3 KB (308 words) - 16:31, 20 October 2022
PB-Assembly
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]] pb-assembly is a collection of PacBio software including the following applications and their dependencies:

2 KB (269 words) - 20:11, 24 August 2022
Bamstats
[[Category:Software]][[Category:Biology]][[Category:NGS]]

2 KB (251 words) - 18:01, 12 August 2022
Magenta
[[Category:Software]][[Category:Phylogenetics]]

3 KB (361 words) - 18:20, 18 August 2022
Miniwdl
[[Category:Software]][[Category:Bioinformatics]]

2 KB (283 words) - 18:55, 1 December 2023
PhyloParser
[[Category:Software]][[Category:Phylogenetics]]

2 KB (245 words) - 18:17, 21 August 2022
FDSTools
[[Category:Software]][[Category:Phylogenetics]]

2 KB (251 words) - 21:34, 27 August 2020
MTR
[[Category:Software]]

2 KB (245 words) - 14:03, 23 June 2021
Deepsig
[[Category:Software]][[Category:Biology]]

2 KB (266 words) - 04:24, 6 December 2022
LncScore
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

3 KB (308 words) - 21:21, 6 December 2019
FLEXLm
[[Category:Software]][[Category:Utility]]

2 KB (263 words) - 16:46, 15 August 2022
Rbp-maps
[[Category:Software]][[Category:Phylogenetics]]

2 KB (242 words) - 18:54, 27 May 2022
LillyMol
[[Category:Software]]

2 KB (236 words) - 14:39, 27 January 2023
Rainbow
[[Category:Software]][[Category:biology]][[Category:sequencing]]

2 KB (254 words) - 21:24, 6 December 2019
Category:File Management
[[Category:Software]]

9 members (0 subcategories, 0 files) - 13:53, 21 October 2022
DDT
[[Category:Software]][[Category:Utility]]

5 KB (754 words) - 19:24, 30 October 2023
RepeatMasker
[[Category:Software]][[Category:Biology]] |{{#vardefine:exe|}} 

2 KB (325 words) - 20:32, 12 August 2022
Photutils
[[Category:Software]][[Category:Astronomy]]

2 KB (271 words) - 13:11, 6 June 2022
GULP
[[Category:Software]][[Category:Material Science]]

3 KB (311 words) - 18:09, 15 August 2022
Knitro
[[Category:Software]][[Category:Math]]

2 KB (286 words) - 19:34, 15 August 2022
ProDy
[[Category:Software]][[Category:Phylogenetics]]

2 KB (294 words) - 19:38, 21 August 2022
Randfold
[[Category:Software]][[Category:Biology]]

2 KB (262 words) - 21:29, 21 August 2022
DISCOVAR de novo
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Assembly]] |{{#vardefine:url|https://software.broadinstitute.org/software/discovar/blog/?page_id=14}}

3 KB (326 words) - 14:41, 15 August 2022
Nubeamdedup
[[Category:Software]][[Category:Phylogenetics]]

2 KB (282 words) - 17:23, 19 August 2022
QDD
[[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]]

4 KB (485 words) - 20:08, 21 August 2022
GATK
[[Category:Software]][[Category:Biology]][[Category:NGS]] |{{#vardefine:exe|1}} 

4 KB (540 words) - 16:53, 15 August 2022
RELION
[[Category:Software]][[Category:Biology]][[Category:Imaging]]

3 KB (434 words) - 21:42, 21 August 2022
Mono
[[Category:Software]][[Category:Linux]][[Category:Programming]]

2 KB (289 words) - 17:41, 15 August 2022
Pygenometracks
[[Category:Software]][[Category:Genomics]][[Category:Biology]]

3 KB (375 words) - 20:54, 18 May 2023
Langdetect
[[Category:Software]]

2 KB (242 words) - 17:01, 23 August 2022
PCRE
[[Category:Software]][[Category:Programming]][[Category:library]] ...ar expression API. The PCRE library is free, even for building proprietary software.

3 KB (307 words) - 12:10, 26 August 2022
Nlr-annotator
[[Category:Software]][[Category:Phylogenetics]]

2 KB (262 words) - 19:28, 31 May 2022
Diamond
[[Category:Software]][[Category:Genomics]][[Category:Biology]] |{{#vardefine:url| http://ab.inf.uni-tuebingen.de/software/diamond/}}

3 KB (307 words) - 14:41, 15 August 2022
PyVCF
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

2 KB (236 words) - 20:08, 21 August 2022
Basic Linux Use
...indows. The major difference is that on Windows you get the system and the software to do what you want by learning to juggle the activities of clicking left,

6 KB (1,054 words) - 14:45, 9 November 2022
DTI-TK
[[Category:Software]][[Category:Biology]][[Category:Neuroscience]]

3 KB (311 words) - 18:51, 12 August 2022
Ucsc-maskoutfa
[[Category:Software]][[Category:Phylogenetics]]

2 KB (237 words) - 20:09, 1 June 2022
Bamaddrg
[[Category:Software]][[Category:Phylogenetics]]

2 KB (302 words) - 20:19, 19 October 2020
Artemis
[[Category:Software]][[Category:Biology]]

3 KB (378 words) - 14:53, 12 August 2022
NCBI BLAST+
[[Category:Software]][[Category:biology]]

3 KB (344 words) - 19:55, 12 August 2022
IsONclust
[[Category:Software]][[Category:Phylogenetics]]

3 KB (307 words) - 13:24, 19 October 2020
Category:Database
[[Category:Software]]

5 members (0 subcategories, 0 files) - 15:33, 6 February 2015
Category:Math
[[Category:Software]]

64 members (1 subcategory, 0 files) - 21:45, 24 October 2022
Dock
[[Category:Software]][[Category:Chemistry]] |{{#vardefine:exe|}} 

2 KB (334 words) - 20:48, 2 August 2021
Stata
[[Category:Software]][[Category:Statistics]][[Category:Statistics]] |{{#vardefine:exe|1}} 

4 KB (621 words) - 15:23, 5 January 2023
Shogun
[[Category:Software]][[Category:Phylogenetics]]

2 KB (246 words) - 18:14, 1 June 2022
Ciriquant
[[Category:Software]][[Category:Phylogenetics]]

2 KB (275 words) - 15:00, 30 March 2022
MPB
[[Category:Software]][[Category:Library]][[Category:Math]] MPB is a free and open-source software package for computing the band structures, or dispersion relations, and ele

3 KB (344 words) - 21:21, 6 December 2019
MITObim
[[Category:Software]][[Category:Phylogenetics]]

3 KB (301 words) - 15:20, 22 April 2020
PRSice
[[Category:Software]][[Category:Phylogenetics]] PRSice (pronounced 'precise') is a Polygenic Risk Score software for calculating, applying, evaluating and plotting the results of polygenic

2 KB (287 words) - 14:26, 1 February 2021
Bcl2fastq
[[Category:Software]][[Category:Biology]][[Category:NGS]] bcl2fastq conversion software can be used to both demultiplex data and

3 KB (328 words) - 18:12, 12 August 2022
VMD
[[Category:Software]][[Category:visualization]][[Category:animation]][[Category:Graphics]] If 3D visualization is required you will need to run this software on a HWGUI partition.

3 KB (384 words) - 17:33, 22 August 2022
Snippy
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

2 KB (237 words) - 14:37, 10 June 2022
Assembly-stats
[[Category:Software]][[Category:Biology]][[Category:Sequencing]][[Category:Genomics]]

2 KB (293 words) - 14:56, 12 August 2022
VASP make
[[Category:Software]]

2 KB (249 words) - 03:23, 17 April 2018
Generic Mapping Tools
[[Category:Software]]

3 KB (336 words) - 16:56, 10 October 2022

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