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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
Software Development
#REDIRECT [[Software Development Policies]]

43 bytes (4 words) - 20:46, 6 June 2022
Installed Software

26 bytes (2 words) - 17:41, 28 September 2017
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
Draft:Software Installation Policies and Guidelines
==Availabile Linux Software installed in ResVault==

2 KB (262 words) - 18:47, 20 February 2023

Page text matches

GenomicTools
[[Category:Software]][[Category:NGS]][[Category:Biology]][[Category:ChIP-Seq]][[Category:RNA-Se

3 KB (385 words) - 18:58, 12 August 2022
CryptoMiniSat
[[Category:Software]][[Category:Math]]

3 KB (325 words) - 14:13, 15 August 2022
CAMP
[[Category:Software]][[Category:Biology]][[Category:Sequencing]]

2 KB (255 words) - 18:00, 23 May 2022
Template:App Module
The modulefile for this software adds the directory with executable files to the shell execution PATH and se

850 bytes (117 words) - 20:45, 16 May 2012
FastStructure
[[Category:Software]][[Category:Biology]][[Category:Genomics]]

3 KB (297 words) - 18:54, 12 August 2022
Purge haplotigs
[[Category:Software]]

3 KB (356 words) - 20:27, 12 August 2022
DECX
[[Category:Software]][[Category:Phylogenetics]]

2 KB (255 words) - 17:54, 26 April 2021
BLASR
[[Category:Software]][[Category:Biology]][[Category:NGS]]

2 KB (236 words) - 18:17, 12 August 2022
BIRDS
[[Category:Software]][[Category:Imaging]][[Category:Workflow Automation]][[Category:Utility]]

2 KB (263 words) - 13:01, 15 August 2022
AMRPlusPlus
[[Category:Software]][[Category:Phylogenetics]]

3 KB (365 words) - 21:19, 6 December 2019
RAPSearch
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

3 KB (304 words) - 21:24, 6 December 2019
Apptests
[[Category:Software]]

3 KB (331 words) - 20:52, 1 November 2023
RiboPicker
[[Category:Software]][[Category:Biology]][[Category:Sequencing]] |{{#vardefine:exe|1}} 

3 KB (377 words) - 21:50, 21 August 2022
Gubbins
[[Category:Software]][[Category:Phylogenetics]]

3 KB (335 words) - 17:28, 15 August 2022
EGSnrc
[[Category:Software]][[Category:Phylogenetics]] ...eleased in 2000, as a complete overhaul of the Electron Gamma Shower (EGS) software package originally developed at the Stanford Linear Accelerator Center (SLA

3 KB (327 words) - 14:57, 15 August 2022
Pvconv
[[Category:Software]]

2 KB (265 words) - 21:12, 24 October 2022
OptiType
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

2 KB (296 words) - 16:37, 10 June 2022
VS Code Remote Development
* By using the software, you agree to

7 KB (1,100 words) - 17:42, 5 March 2024
DRAP
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

2 KB (280 words) - 21:20, 6 December 2019
Asaq
[[Category:Software]][[Category:Alignment]][[Category:Sequencing]][[Category:Phylogenetics]] Please cite the following papers if you use Armadillo in your research and/or software.

3 KB (374 words) - 15:10, 1 June 2022
Category:Annotation
[[Category:Software]]

8 members (0 subcategories, 0 files) - 19:54, 22 August 2022
Pypaftol
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Phylogenetics]]

3 KB (307 words) - 14:11, 9 April 2024
FreeBayes
[[Category:Software]][[Category:Biology]][[Category:Genomics]] |{{#vardefine:exe|}} 

2 KB (302 words) - 18:55, 12 August 2022
IGB
[[Category:Software]][[Category:Biology]][[Category:Genomics]]

2 KB (257 words) - 18:41, 15 August 2022
Humann2
[[Category:Software]][[Category:Phylogenetics]]

3 KB (348 words) - 22:26, 27 August 2020
Vermouth-martinize
[[Category:Software]][[Category:Phylogenetics]]

3 KB (323 words) - 14:21, 1 November 2021
RNAmmer
[[Category:Software]][[Category:Biology]][[Category:RNA-Seq]]

3 KB (328 words) - 17:35, 10 June 2022
RNAhybrid
[[Category:Software]][[Category:Biology]][[Category:Genomics]]

2 KB (285 words) - 20:56, 12 August 2022
Centrifuge
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

3 KB (355 words) - 21:05, 6 December 2019
Draft:UFRC Help and Documentation Testa
==[[:Category:Applications|Software and Reference Data]] [[Image:Software.png|left|frameless|upright=0.1]]==

4 KB (522 words) - 17:49, 31 January 2023
Taxtastic
[[Category:Software]][[Category:biology]][[Category:Genomics]]

2 KB (263 words) - 15:45, 19 August 2022
Pybedtools
[[Category:Software]][[Category:Phylogenetics]]

2 KB (263 words) - 13:31, 6 October 2021
REAPR
[[Category:Software]][[Category:Biology]][[Category:Assembly]] |{{#vardefine:url|http://www.sanger.ac.uk/resources/software/reapr/#t_2}}

3 KB (320 words) - 21:35, 21 August 2022
Meryl
[[Category:Software]][[Category:Phylogenetics]]

2 KB (254 words) - 22:26, 8 September 2020
Nanocomp
[[Category:Software]][[Category:programming]][[Category:sequencing]]

2 KB (282 words) - 12:22, 26 August 2022
ETE3
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] This is a GUI software. Follow the instructions at https://wiki.rc.ufl.edu/doc/GUI_Programs

3 KB (400 words) - 19:13, 10 June 2022
MiRDP2
[[Category:Software]][[Category:Biology]][[Category:Genomics]]

3 KB (328 words) - 18:09, 31 May 2022
PHASE
[[Category:Software]][[Category:Phylogenetics]] In all cases, please specify the version of the software used, and any deviations from the default options.

2 KB (276 words) - 18:09, 21 August 2022
Mlpack
[[Category:Software]][[Category:Library]] ...M. Lozhnikov, Y. Mentekidis, S. Ghaisas, S. Zhang. Journal of Open Source Software 3:26, 2018.]

3 KB (301 words) - 19:43, 15 December 2020
Pyfaidx
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]]

3 KB (340 words) - 19:58, 21 August 2022
MISO
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]][[Category:RNA-

3 KB (390 words) - 20:44, 18 August 2022
Fqtools
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]] fqtools is a software suite for fast processing of FASTQ files. Various file manipulations are su

3 KB (359 words) - 16:47, 15 August 2022
MasHmap
[[Category:Software]][[Category:Phylogenetics]]

3 KB (359 words) - 17:28, 27 May 2022
Haphpipe
[[Category:Software]][[Category:Phylogenetics]][[Category:Biology]]

3 KB (405 words) - 16:40, 14 March 2023
Category:Simulation
[[Category:Software]] Hardware or software environment simulation.

16 members (0 subcategories, 0 files) - 18:44, 7 July 2017
Nanodisco
[[Category:Software]][[Category:Phylogenetics]]

3 KB (326 words) - 14:37, 27 August 2021
SOAPaligner
[[Category:Software]][[Category:Phylogenetics]] ...(Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast

3 KB (334 words) - 21:24, 6 December 2019
ACTC
[[Category:Software]][[Category:Biology]]

2 KB (234 words) - 14:36, 7 April 2023
RGIS
[[Category:Software]][[Category:Geospatial]] ...software. RiverGIS is not intended to replace or compete with existing GIS software. It was designed to complement existing GIS packages (like ARC/INFO) and pr

3 KB (370 words) - 20:27, 24 August 2022
MCNP
[[Category:Software]][[Category:Physics]] ...message from RSICC’s Request History tool that contains a list all of the software for which you have been licensed to the [[Remote_Support#Email|User Support

3 KB (422 words) - 21:39, 4 April 2024
Racon
[[Category:Software]][[Category:Phylogenetics]]

3 KB (364 words) - 21:24, 21 August 2022
Sc-im
[[Category:Software]][[Category:Visualization]][[Category:Utility]]

2 KB (272 words) - 22:07, 21 August 2022
Pyweka
[[Category:Software]][[Category:Phylogenetics]]

2 KB (265 words) - 17:35, 1 June 2022
MODELTEST
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

2 KB (277 words) - 16:18, 10 June 2022
InStruct
[[Category:Software]][[Category:Phylogenetics]]

2 KB (254 words) - 18:00, 11 March 2020
ReCOGnizer
[[Category:Software]][[Category:Phylogenetics]]

3 KB (327 words) - 17:03, 3 December 2020
Picard-tools
[[Category:Software]][[Category:Biology]][[Category:NGS]] |{{#vardefine:exe|1}} 

6 KB (882 words) - 15:25, 27 January 2023
VeryFastTree
[[Category:Software]][[Category:Phylogenetics]]

3 KB (329 words) - 21:03, 12 February 2021
Oases
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Assembly]] |{{#vardefine:exe|}} 

2 KB (293 words) - 17:25, 19 August 2022
PHAST
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] PHAST is a freely available software package for comparative and evolutionary genomics. It consists of about hal

3 KB (320 words) - 17:17, 10 June 2022
Dragonflye
[[Category:Software]][[Category:Sequencing]][[Category:Genomics]] https://github.com/rpetit3/dragonflye#software-included-19

2 KB (283 words) - 20:18, 12 April 2022
Boost
[[Category:Software]][[Category:Library]][[Category:Programming]][[Category:Compiler]]

3 KB (350 words) - 13:06, 15 August 2022
MOTU
[[Category:Software]][[Category:Biology]][[Category:Genomics]] |{{#vardefine:url|http://www.bork.embl.de/software/mOTU/}}

3 KB (328 words) - 12:00, 19 August 2022
Glactools
[[Category:Software]][[Category:Phylogenetics]]

2 KB (247 words) - 15:07, 20 May 2020
Merge peaks
[[Category:Software]][[Category:Workflow Automation]]

2 KB (254 words) - 18:51, 15 August 2022
MIA
[[Category:Software]][[Category:Biology]][[Category:NGS]]

3 KB (347 words) - 19:52, 12 August 2022
HPG Computation
...open a support ticket to request RC to install the software in one of our software environments if it will be widely used. ==Using installed software==

5 KB (760 words) - 17:35, 22 April 2024
Booster
[[Category:Software]][[Category:Phylogenetics]]

2 KB (283 words) - 21:11, 6 December 2019
Trim Galore
[[Category:Software]][[Category:Biology]][[Category:NGS]]

4 KB (512 words) - 20:52, 12 August 2022
Grib api
[[Category:Software]][[Category:Compiler]][[Category:Library]] |{{#vardefine:url|https://software.ecmwf.int/wiki/display/GRIB}}

2 KB (278 words) - 17:22, 15 August 2022
RGI
[[Category:Software]][[Category:Phylogenetics]]

3 KB (352 words) - 21:24, 6 December 2019
Plink
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]][[Category:Genomics]]

3 KB (342 words) - 20:25, 12 August 2022
Unanimity
[[Category:Software]][[Category:Programming]][[Category:Library]][[Category:Compiler]]

2 KB (268 words) - 17:48, 15 August 2022
FastPlast
[[Category:Software]][[Category:Phylogenetics]]

2 KB (288 words) - 20:23, 23 May 2022
Modules Basic Usage
...the latest or the default version of the module and be able to execute the software is 'module load <application>'. For instance, if the module is called '''nc ...spective branches. E.g., if you need to load the module for the "espresso" software that was built with MVAPICH2 support using Intel Compiler version 11.1 you

5 KB (745 words) - 16:07, 13 February 2023
Rolling Upgrade from RHEL7 to RHEL8
...at Enterprise Linux version 7 (RHEL-7) to version 8 (RHEL-8). The upgraded software environment includes updates to important components including, but not lim Some programs/workflows run in the updated software environment without any modification, and some require recompilation or ada

1 KB (164 words) - 16:06, 28 September 2023
Strelka
[[Category:Software]][[Category:Biology]][[Category:Genomics]]

3 KB (369 words) - 14:24, 10 October 2023
Finder
[[Category:Software]] independent software that generatess gene annotations in GTF format. finder

3 KB (345 words) - 16:42, 15 August 2022
Olego
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]]

3 KB (309 words) - 17:44, 19 August 2022
DeNoGAP
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]][[Category:NGS]]

2 KB (272 words) - 21:20, 6 December 2019
PhiSpy
[[Category:Software]][[Category:Phylogenetics]]

2 KB (291 words) - 21:23, 6 December 2019
Lambda
[[Category:Software]][[Category:Biology]][[Category:Sequencing]][[Category:Phylogenetics]]

2 KB (279 words) - 21:21, 6 December 2019
Pbpigeon
[[Category:Software]][Category:Biology]]

2 KB (275 words) - 22:37, 21 January 2024
Category:Alignment
[[Category:Biology]][[Category:Software]]

24 members (0 subcategories, 0 files) - 15:24, 23 August 2022
Fairseq
[[Category:Software]][[Category:Modeling]][[Category:Machine Learning]]

3 KB (296 words) - 15:18, 15 August 2022
FASTphase
[[Category:Software]][[Category:Phylogenetics]] |{{#vardefine:url|http://stephenslab.uchicago.edu/software.html#fastphase}}

2 KB (282 words) - 21:59, 27 August 2020
RepeatAnalysisTools
[[Category:Software]] @software{tange_2021_5013933,

4 KB (430 words) - 16:55, 15 December 2022
BRIG
[[Category:Software]][[Category:Biology]][[Category:Genomics]]

2 KB (278 words) - 16:25, 10 June 2022
CoMap
[[Category:Software]][[Category:Biology]][[Category:Genomics]]

3 KB (378 words) - 18:39, 12 August 2022
Pigz
[[Category:Software]][[Category:Compression]]

2 KB (245 words) - 21:23, 6 December 2019
SuperCRUNCH
[[Category:Software]][[Category:Phylogenetics]]

4 KB (499 words) - 14:47, 11 May 2020
Vcfanno
[[Category:Software]][[Category:biology]][[Category:phylogenetics]]

2 KB (291 words) - 21:29, 6 December 2019
Maker
[[Category:Software]][[Category:Biology]] |{{#vardefine:url|http://www.yandell-lab.org/software/maker.html}}

3 KB (387 words) - 18:20, 18 August 2022
RSeQC
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]]

3 KB (328 words) - 17:48, 10 June 2022
KMC
[[Category:Software]][[Category:Phylogenetics]]

3 KB (343 words) - 14:34, 4 September 2020
Conefor
[[Category:Software]][[Category:Biology]] Conefor is a software package that allows quantifying the importance of habitat areas and links f

3 KB (303 words) - 14:33, 2 May 2023
Roary
[[Category:Software]][[Category:Biology]][[Category:Genomics]]

3 KB (308 words) - 17:13, 10 June 2022
DSSP
[[Category:Software]][[Category:Molecular Dynamics]] |{{#vardefine:exe|}} 

2 KB (297 words) - 19:51, 13 June 2022
Wgsim
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]

3 KB (343 words) - 21:29, 6 December 2019
SQANTI2
[[Category:Software]][[Category:Phylogenetics]]

2 KB (239 words) - 18:47, 1 June 2022

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