Search results

Jump to navigation Jump to search

  • WDSSII
    [[Category:Software]][[Category:Climate]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    2 KB (299 words) - 20:05, 24 August 2022
  • Ltr finder
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    3 KB (416 words) - 20:21, 15 August 2022
  • Shustring
    [[Category:Software]][[Category:Biology]][[Category:Sequencing]]
    2 KB (237 words) - 14:55, 10 June 2022
  • Quake
    [[Category:Software]][[Category:Biology]][[Category:Sequencing]] |{{#vardefine:url|http://www.cbcb.umd.edu/software/quake/}}
    3 KB (367 words) - 18:50, 10 June 2022
  • V-Phaser
    [[Category:Software]][[Category:biology]][[Category:phylogenetics]]
    3 KB (390 words) - 20:07, 27 May 2022
  • Circompara2
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (283 words) - 21:36, 1 April 2022
  • Package-GFE
    [[Category:Software]][[Category:Biology]][[Category:Genomics]] This software package is for estimating allele and genotype frequencies from nucleotide r
    2 KB (280 words) - 16:45, 10 June 2022
  • 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
  • CGATools
    [[Category:Software]][[Category:Biology]][[Category:NGS]]
    2 KB (291 words) - 13:26, 15 August 2022
  • Arcashla
    [[Category:Software]]
    2 KB (250 words) - 19:33, 24 July 2023
  • MKL
    [[Category:Software]][[Category:Library]][[Category:Math]][[Category:Programming]][[Category:Co |{{#vardefine:url|https://software.intel.com/en-us/mkl}}
    3 KB (378 words) - 19:14, 24 August 2022
  • Assembly-stats
    [[Category:Software]][[Category:Biology]][[Category:Sequencing]][[Category:Genomics]]
    2 KB (293 words) - 14:56, 12 August 2022
  • Xlsx2csv
    [[Category:Software]]
    2 KB (241 words) - 20:08, 24 October 2022
  • Svtyper
    [[Category:Software]]
    3 KB (360 words) - 14:04, 3 October 2022
  • 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
  • Platypus
    [[Category:Software]][[Category:Biology]][[Category:NGS]]
    3 KB (435 words) - 19:21, 10 June 2022
  • AGAT
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (346 words) - 22:01, 15 July 2020
  • Arriba
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (363 words) - 14:07, 1 April 2021
  • MGEScan
    [[Category:Software]][[Category:Biology]][[Category:Genomics]]
    2 KB (299 words) - 16:58, 10 June 2022
  • Necklace
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] ...ovo assembly, in addition to using the reference annotation. Necklace is a software pipeline to run genome-guided and de novo assembly and combine the resultin
    3 KB (312 words) - 21:22, 6 December 2019
  • Nanodisco
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (326 words) - 14:37, 27 August 2021
  • TRANSIT
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (279 words) - 21:29, 6 December 2019
  • ANNOVAR
    [[Category:Software]][[Category:Biology]][[Category:Genomics]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    4 KB (545 words) - 14:16, 12 August 2022
  • Dammit
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] ..., the existing solutions are overly complicated or rely on crappy non-free software.
    2 KB (279 words) - 21:20, 6 December 2019
  • Category:Physics
    [[Category:Software]]
    21 members (0 subcategories, 0 files) - 15:38, 19 September 2014
  • EDTA
    [[Category:Software]][[Category:Genomics]]
    4 KB (474 words) - 21:27, 14 September 2023
  • Add New App Page
    ...app module name e.g. "foo" into the text box and click on the "Create new software page" button. Edit the resulting page as necessary.
    245 bytes (44 words) - 17:34, 3 June 2022
  • SHARCGS
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:De Novo]]
    3 KB (313 words) - 22:42, 21 August 2022
  • Pathoscope
    [[Category:Software]][[Category:Sequencing]][[Category:Genomics]][[Category:Biology]]
    3 KB (323 words) - 17:02, 21 August 2022
  • LINKS
    [[Category:Software]][[Category:Biology]][[Category:Genomics]]
    2 KB (274 words) - 16:16, 10 June 2022
  • CutRunTools
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (266 words) - 22:20, 26 August 2020
  • Lazypipe
    [[Category:Software]]
    4 KB (507 words) - 16:54, 14 December 2022
  • MiRanda
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (278 words) - 21:21, 6 December 2019
  • PROVEAN
    [[Category:Software]][[Category:Biology]][[Category:Genomics]] PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impa
    3 KB (350 words) - 20:27, 12 August 2022
  • GetOrganelle
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (275 words) - 21:21, 6 December 2019
  • Structure
    [[Category:Software]][[Category:Biology]][[Category:Genomics]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    2 KB (325 words) - 16:03, 22 August 2022
  • CAVIAR
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (275 words) - 21:17, 6 December 2019
  • 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
  • DALIGNER
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (238 words) - 14:28, 15 August 2022
  • GRACKLE
    [[Category:Software]][[Category:Library]][[Category:Compiler]][[Category:Astronomy]]
    2 KB (294 words) - 17:18, 15 August 2022
  • ParlAI
    [[Category:Software]][[Category:Phylogenetics]] title={ParlAI: A Dialog Research Software Platform},
    3 KB (301 words) - 15:55, 21 July 2021
  • 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
  • Rosetta
    [[Category:Software]][[Category:Biology]][[Category:Modeling]][[Category:Structure]] Rosetta is the premier software suite for modeling macromolecular
    3 KB (302 words) - 20:37, 10 June 2022
  • Category:Assembly
    [[Category:Biology]][[Category:NGS]][[Category:Software]] Short Sequence Assembly software.
    20 members (0 subcategories, 0 files) - 15:24, 23 August 2022
  • Sim4Life
    [[Category:Software]][[Category:Biology]][[Category:Simulation]]
    2 KB (271 words) - 18:20, 1 June 2022
  • EnTAP
    [[Category:Software]][[Category:biology]][[Category:phylogenetics]]
    2 KB (236 words) - 21:20, 6 December 2019
  • C-wap
    [[Category:Software]][[Category:Sequencing]][[Category:Genomics]][[Category:Biology]]
    2 KB (281 words) - 13:16, 15 August 2022
  • BUSCO
    [[Category:Software]][[Category:Biology]][[Category:Genomics]]
    5 KB (607 words) - 19:38, 27 March 2023
  • Macaulay2
    [[Category:Software]][[Category:Phylogenetics]] A software system for research in algebraic geometry
    2 KB (246 words) - 20:23, 15 August 2022
  • Nextclade
    [[Category:Software]]
    2 KB (260 words) - 19:03, 12 January 2023
  • Hylite
    [[Category:Software]]
    3 KB (325 words) - 21:51, 24 February 2023
  • Mxnet
    [[Category:Software]][[Category:healthcare]]
    2 KB (265 words) - 22:02, 10 October 2022
  • MCNPX
    [[Category:Software]][[Category:Physics]]
    2 KB (221 words) - 18:28, 18 August 2022
  • NucleoATAC
    [[Category:Software]][[Category:biology]]
    2 KB (276 words) - 20:08, 12 August 2022
  • Spacemake
    [[Category:Software]][[Category:Sequencing]]
    2 KB (249 words) - 22:12, 22 September 2022
  • Flye
    [[Category:Software]][[Category:Biology]][[Category:NGS]]
    3 KB (317 words) - 21:20, 6 December 2019
  • PLEK
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (241 words) - 14:57, 10 June 2022
  • SourceTracker2
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (357 words) - 14:19, 14 September 2020
  • Comp-D MPI
    [[Category:Software]][[Category:Statistics]]
    2 KB (264 words) - 16:54, 9 June 2022
  • AdmixTools
    [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]] ADMIXTOOLS (Patterson et al. 2012) is a software package that supports formal tests of whether admixture occurred, and makes
    3 KB (400 words) - 20:50, 11 August 2022
  • BOLT-LMM
    [[Category:Software]][[Category:Phylogenetics]] The BOLT-LMM software package currently consists of two main algorithms, the BOLT-LMM algorithm f
    2 KB (289 words) - 16:24, 2 January 2020
  • Category:Graphics
    [[Category:Software]]
    13 members (0 subcategories, 0 files) - 18:46, 10 August 2012
  • NANO
    [[Category:Software]][[Category:Programming]]
    3 KB (360 words) - 19:24, 29 November 2022
  • ROOT
    [[Category:Software]][[Category:Data Science]]
    3 KB (358 words) - 16:48, 21 August 2022
  • PBGCpp
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (229 words) - 20:05, 31 May 2022
  • XZ
    [[Category:Software]][[Category:compression]][[Category:library]] XZ Utils is free general-purpose data compression software with a high compression ratio. XZ Utils were written for POSIX-like systems
    2 KB (287 words) - 14:19, 27 May 2022
  • PBCCS
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (245 words) - 17:07, 21 August 2022
  • Skmer
    [[Category:Software]][[Category:genomics‏‎]][[Category:Biology]]
    2 KB (260 words) - 13:31, 15 August 2022
  • ReFrame
    [[Category:Software]][[Category:Performance Analysis]][[Category:Utility]]
    2 KB (240 words) - 21:40, 21 August 2022
  • MongoDB
    [[Category:Software]][[Category:Database]]
    3 KB (340 words) - 19:22, 11 February 2021
  • Amuse
    [[Category:Software]][[Category:Astronomy]] AMUSE is an Astrophysical Multipurpose Software Environment. Within AMUSE different existing numerical codes are incorporat
    2 KB (287 words) - 20:34, 15 August 2022
  • MountainSort
    [[Category:Software]][[Category:Library]] MountainSort (a component of MountainLab) is spike sorting software developed by Jeremy Magland, Alex Barnett, and Leslie Greengard at the Cent
    3 KB (309 words) - 21:22, 6 December 2019
  • PEAR
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Genomics]] |{{#vardefine:url|http://www.exelixis-lab.org/web/software/pear}}
    3 KB (312 words) - 17:25, 21 August 2022
  • BoltzTraP
    [[Category:Software]][[Category:Physics]]
    2 KB (279 words) - 16:19, 10 June 2022
  • VDJtools
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (280 words) - 21:29, 6 December 2019
  • AutoDock-GPU
    [[Category:Software]][[Category:Chemistry]]
    3 KB (332 words) - 15:25, 12 August 2022
  • Matlab GUI Example
    [[Category:Software]]
    3 KB (375 words) - 21:32, 24 October 2022
  • Knime
    [[Category:Software]] KNIME Analytics Platform is an open source software that allows users to access, blend, analyze, and visualize data, without an
    3 KB (318 words) - 14:46, 9 June 2023
  • DSRC
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (252 words) - 14:27, 17 February 2021
  • CASAVA
    [[Category:Software]][[Category:Biology]][[Category:NGS]] |{{#vardefine:url|http://www.illumina.com/software/genome_analyzer_software.ilmn}}
    3 KB (340 words) - 18:23, 12 August 2022
  • HALC
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (265 words) - 21:20, 6 December 2019
  • Camino
    [[Category:Software]][[Category:Imaging]][[Category:Biology]][[Category:Neuroscience]] Camino is an open-source software toolkit for diffusion MRI processing. The toolkit implements standard techn
    3 KB (291 words) - 18:22, 12 August 2022
  • GAL
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (250 words) - 21:20, 6 December 2019
  • EMBOSS
    [[Category:Software]][[Category:Biology]] ...to a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.
    3 KB (372 words) - 15:01, 15 August 2022
  • USEARCH
    [[Category:Software]][[Category:Biology]][[Category:Alignment]][[Category:Sequencing]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    4 KB (559 words) - 17:19, 22 August 2022
  • Zstd
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (264 words) - 17:55, 22 August 2022
  • Rascaf
    [[Category:Software]][[Category:Biology]]
    3 KB (415 words) - 21:30, 21 August 2022
  • Merqury
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (306 words) - 13:54, 12 August 2020
  • TGSGapCloser
    [[Category:Software]][[Category:Phylogenetics]] A gap-closing software tool that uses error-prone long reads generated by third-generation-sequenc
    3 KB (321 words) - 15:35, 20 April 2021
  • TensorFlow
    [[Category:Software]][[Category:Library]][[Category:Math]] TensorFlow is an open-source software library that is commonly used for implementing artificial neural networks a
    6 KB (790 words) - 15:25, 14 December 2022
  • Bertini
    [[Category:Software]][[Category:Math]] Software for solving polynomial systems
    2 KB (248 words) - 12:48, 15 August 2022
  • SCIrun
    [[Category:Software]][[Category:Phylogenetics]] |{{#vardefine:url|https://www.sci.utah.edu/cibc-software/scirun.html}}
    3 KB (344 words) - 22:09, 21 August 2022
  • Dancemapper
    [[Category:Software]][[Category:Machine Learning]]
    2 KB (252 words) - 22:13, 6 March 2023
  • MetaPhlAn2
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    3 KB (319 words) - 19:28, 2 June 2022
  • Installing Personal Python Modules
    [[Category:Python]][[Category:Software]] ...use this guide to install a small personal python module or a python-based software package that is packaged with distutils i.e. you install it with '<code>pyt
    2 KB (243 words) - 14:51, 10 February 2023
  • Unicycler
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (292 words) - 21:29, 6 December 2019
  • Deepvariant
    [[Category:Software]]
    3 KB (356 words) - 13:17, 16 April 2024
  • SInC
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (278 words) - 21:24, 6 December 2019
  • Miniwdl
    [[Category:Software]][[Category:Bioinformatics]]
    2 KB (283 words) - 18:55, 1 December 2023
  • Bigslice
    [[Category:Software]][[Category:Biology]][[Category:Genomics]]
    3 KB (295 words) - 21:25, 14 September 2023
  • Stampy
    [[Category:Software]][[Category:Biology]][[Category:Sequencing]]
    3 KB (327 words) - 20:45, 12 August 2022
  • Dtiprep
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (290 words) - 21:50, 27 August 2020
  • MTR
    [[Category:Software]]
    2 KB (245 words) - 14:03, 23 June 2021
  • NucDiff
    [[Category:Software]][[Category:Phylogenetics]] ...ral.com/articles/10.1186/gb-2004-5-2-r12 Kurtz S et al. Versatile and open software for comparing large genomes. Genome Biol. 2004;5(2):R12. doi 10.1186/gb-200
    3 KB (315 words) - 21:22, 6 December 2019
  • QUAST
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]][[Category:RNA-
    3 KB (361 words) - 21:01, 21 August 2022
  • Falco
    [[Category:Software]] Falco is a program emulation of the popular FastQC software to check large sequencing reads for common problems.
    2 KB (283 words) - 14:11, 21 October 2022
  • Perl
    [[Category:Software]][[Category:Language]][[Category:Programming]] |{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
    5 KB (811 words) - 17:56, 2 January 2023
  • BYOBU
    [[Category:Software]][[Category:Shell]]
    3 KB (313 words) - 19:50, 11 July 2022
  • Kmcos
    [[Category:Software]][[Category:Chemistry]]
    2 KB (255 words) - 13:54, 30 April 2024
  • FastUniq
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    3 KB (301 words) - 16:37, 15 August 2022
  • MEGASAT
    [[Category:Software]][[Category:Phylogenetics]] MEGASAT is a software tool that can automatically infer genotypes from high-throughput microsatel
    2 KB (278 words) - 13:22, 28 August 2020
  • Hal
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (366 words) - 18:11, 15 August 2022
  • Distruct
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (267 words) - 21:20, 6 December 2019
  • Vim
    [[Category:Software]][[Category:Programming]][[Category:Language]]
    3 KB (320 words) - 18:56, 21 August 2022
  • TURBOMOLE
    [[Category:Software]][[Category:Chemistry]] TURBOMOLE is a licensed software. To use it, please provide your license. We will set the file permissions a
    3 KB (369 words) - 17:42, 15 August 2022
  • QRNA
    [[Category:Software]][[Category:Phylogenetics]] |{{#vardefine:url|http://eddylab.org/software/qrna/}}
    2 KB (251 words) - 17:39, 1 June 2022
  • Gawk
    [[Category:Software]][[Category:Utility]] |{{#vardefine:url|https://www.gnu.org/software/gawk/}}
    3 KB (356 words) - 16:55, 15 August 2022
  • BEAGLE
    [[Category:Software]][[Category:Biology]][[Category:Genomics]] BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thou
    5 KB (615 words) - 15:36, 14 December 2022
  • SAS
    [[Category:Software]][[Category:Statistics]][[Category:Data Science]] |{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
    5 KB (775 words) - 13:48, 15 September 2023
  • MetaPhysicl
    [[Category:Software]][[Category:Math]][[Category:Astronomy]][[Category:Simulation]]
    2 KB (247 words) - 19:28, 18 August 2022
  • SLAW
    [[Category:Software]][[Category:Chemistry]][[Category:Spectroscopy]]
    3 KB (389 words) - 23:49, 21 August 2022
  • LAMP
    [[Category:Software]][[Category:Biology]][[Category:Genomics]] LAMP is a software package for the inference of locus-specific ancestry in recently admixed po
    2 KB (245 words) - 19:29, 12 August 2022
  • Slurm
    [[Category:Software]][[Category:Scheduler]] ...a fair chance of using the resources without interfering with each other. Software called a resource manager and a scheduler are required to fulfill the above
    5 KB (763 words) - 17:37, 5 March 2024
  • Training
    ===Intel Software Tools Technical Webinar Series=== ...n information is available [http://software.intel.com/en-us/articles/intel-software-tools-technical-webinar-series here].
    3 KB (484 words) - 13:21, 10 January 2023
  • Glog
    [[Category:Software]][[Category:Web]][[Category:Library]]
    2 KB (269 words) - 17:10, 15 August 2022
  • AtomEye
    [[Category:Software]][[Category:Material Science]] AtomEye is free atomistic visualization software for all major UNIX platforms. It is based on a newly developed graphics cor
    3 KB (351 words) - 15:21, 12 August 2022
  • Category:Sequencing
    Sequencing Software on HiPerGator [[Category:Software]][[Category:Research]]
    146 members (0 subcategories, 0 files) - 21:43, 24 October 2022
  • PRANK
    [[Category:Software]][[Category:Biology]][[Category:Alignment]]
    2 KB (271 words) - 20:25, 12 August 2022
  • PyVista
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (344 words) - 13:56, 25 September 2020
  • Plotsr
    [[Category:Software]]
    2 KB (271 words) - 20:00, 5 August 2022
  • Fastq-tools
    [[Category:Software]][[Category:Biology]][[Category:NGS]]
    3 KB (306 words) - 17:31, 10 June 2022
  • Qcat
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (306 words) - 16:17, 23 January 2020
  • Krona
    [[Category:Software]][[Category:Biology]]
    2 KB (254 words) - 19:29, 12 August 2022
  • Intel MPI
    [[Category:Software]][[Category:Programming]][[Category:Programming]][[Category:Library]] |{{#vardefine:url|https://software.intel.com/en-us/intel-mpi-library}}
    3 KB (297 words) - 12:01, 26 August 2022
  • FFmpeg
    [[Category:Software]][[Category:Audio]][[Category:Visualization]]
    2 KB (252 words) - 16:41, 15 August 2022
  • BUCKy
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    3 KB (386 words) - 13:15, 15 August 2022
  • W2rap-contigger
    [[Category:Software]][[Category:biology]][[Category:genomics]]
    2 KB (246 words) - 21:29, 6 December 2019
  • 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
  • Spidey
    [[Category:Software]][[Category:Biology]][[Category:Genomics]]
    2 KB (295 words) - 20:44, 12 August 2022
  • Slamdunk
    [[Category:Software]][[Category:Phylogenetics]] SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis
    3 KB (294 words) - 20:55, 27 May 2022
  • QAPA
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (305 words) - 16:54, 15 January 2021
  • Phenix
    [[Category:Software]][[Category:Material Science]] PHENIX is a software suite for the automated determination of macromolecular structures using X-
    3 KB (325 words) - 18:12, 21 August 2022
  • MIGRATE-N
    [[Category:Software]][[Category:Genomics]][[Category:Biology]] |{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
    5 KB (636 words) - 16:05, 22 December 2022
  • Create SSH Keys Using Putty
    ==Prerequisite software== Here is a list of the software you will need to be installed on your local machine to start using key-base
    7 KB (1,195 words) - 13:39, 26 June 2023
  • PennCNV
    [[Category:Software]][[Category:Phylogenetics]] PennCNV is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays.
    4 KB (474 words) - 21:23, 6 December 2019
  • Gffread
    [[Category:Software]][[Category:Biology]]
    2 KB (242 words) - 19:02, 12 August 2022
  • Category:Performance Analysis
    [[Category:Software]]
    10 members (0 subcategories, 0 files) - 19:52, 22 August 2022
  • Lrgapcloser
    [[Category:Software]][[Category:Biology]]
    3 KB (326 words) - 19:30, 12 August 2022
  • Micop
    [[Category:Software]][[Category:Genomics]]
    2 KB (269 words) - 16:40, 27 September 2022
  • Conda
    [[Category:Software]][[Category:Programming]]
    16 KB (2,392 words) - 20:14, 16 April 2024
  • AI Reference Datasets
    You may need to use the full path /blue/data/ai for software applications to find the file.
    2 KB (256 words) - 15:03, 28 September 2021
  • OpenFOAM
    [[Category:Software]][[Category:Fluid Dynamics]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    3 KB (445 words) - 14:20, 15 December 2022
  • PyPHLAWD
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (263 words) - 21:24, 6 December 2019
  • CIMS
    [[Category:Software]][[Category:Biology]][[Category:Genomics]]
    3 KB (315 words) - 17:21, 10 June 2022
  • MTG2
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (310 words) - 21:21, 6 December 2019
  • FALCON fc run cfg
    [[Category:Software]]
    2 KB (248 words) - 20:31, 2 August 2021
  • Texlive
    [[Category:Software]][[Category:Documentation]]
    2 KB (267 words) - 16:34, 22 August 2022
  • CGView
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (351 words) - 19:39, 23 May 2022
  • Biology
    ...ends on the stability of the four main corner stones - hardware resources, software availability and support, training and documentation, and direct consulting ==Software==
    4 KB (665 words) - 21:23, 14 December 2022
  • Gcnenv
    [[Category:Software]][[Category:Math]]
    2 KB (243 words) - 19:38, 20 June 2023
  • Geopython
    [[Category:Software]][[Category:Programming]][[Category:Geospatial]]
    2 KB (246 words) - 12:22, 26 August 2022
  • SCRIPTURE
    [[Category:Software]][[Category:Biology]][[Category:Genomics]] |{{#vardefine:url|http://software.broadinstitute.org/software/scripture/}}
    3 KB (302 words) - 20:36, 12 August 2022
  • COLMAP
    [[Category:Software]][[Category:Modeling]] ...eatures for reconstruction of ordered and unordered image collections. The software is licensed under the new BSD license. If you use this project for your res
    2 KB (290 words) - 16:53, 6 June 2022
  • PATRIC
    [[Category:Software]][[Category:Machine Learning]] PATRIC is an integration of different types of data and software tools that support research on bacterial pathogens. The typical biologist s
    3 KB (390 words) - 16:04, 6 June 2022
  • ARKS
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (285 words) - 21:15, 6 December 2019
  • Ansible
    [[Category:Software]][[Category:Workflow Automation]]
    3 KB (348 words) - 14:17, 12 August 2022
  • Quickmerge
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (325 words) - 21:24, 6 December 2019
  • Novoalign
    [[Category:Software]][[Category:Biology]][[Category:NGS]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    3 KB (370 words) - 17:19, 19 August 2022
  • Unrar
    [[Category:Software]][[Category:utility]]
    2 KB (239 words) - 19:16, 3 June 2022
  • Ncbi-genome-download
    [[Category:Software]][[Category:Biology]][[Category:Genomics]]
    2 KB (241 words) - 20:42, 7 February 2024
  • ATAT
    [[Category:Software]][[Category:Material Science]]
    2 KB (247 words) - 15:18, 12 August 2022
  • FMRIPrep
    [[Category:Software]][[Category:Data Mining]]
    2 KB (288 words) - 16:47, 17 October 2023
  • Rbp-maps
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (242 words) - 18:54, 27 May 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
  • Guideseq
    [[Category:Software]]
    2 KB (259 words) - 18:08, 15 August 2022
  • Category:Language
    [[Category:Software]]
    22 members (0 subcategories, 0 files) - 15:37, 3 June 2022
  • Gmap
    [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]] |{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
    3 KB (450 words) - 17:11, 15 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
  • PETSc
    [[Category:Software]][[Category:Math]] ...ferential equations. It is the world’s most widely used parallel numerical software library for partial differential equations and sparse matrix computations.
    3 KB (337 words) - 15:25, 19 August 2022
  • Phylopypruner
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (263 words) - 18:41, 27 May 2022
  • LAPACK
    [[Category:Software]][[Category:Library]][[Category:Programming]][[Category:Compiler]] LAPACK is a standard software library for numerical linear algebra. It provides routines for solving syst
    2 KB (286 words) - 17:43, 15 August 2022
  • ProDy
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (294 words) - 19:38, 21 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
  • GFOLD
    [[Category:Software]][[Category:Biology]][[Category:RNA-Seq]]
    3 KB (388 words) - 18:54, 10 June 2022
  • Torch-geometric
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (241 words) - 19:43, 1 June 2022
  • Python-core
    [[Category:Software]][[Category:Language]][[Category:Programming]]
    3 KB (318 words) - 20:04, 21 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
  • FastML
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    3 KB (312 words) - 18:54, 12 August 2022
  • Zagros
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] |{{#vardefine:url|http://smithlabresearch.org/software/zagros/}}
    2 KB (289 words) - 17:54, 22 August 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
  • Mpinterfaces
    [[Category:Software]][[Category:Math]]
    2 KB (279 words) - 12:27, 19 August 2022
  • Pygenometracks
    [[Category:Software]][[Category:Genomics]][[Category:Biology]]
    3 KB (375 words) - 20:54, 18 May 2023
  • ClustalO
    [[Category:Software]][[Category:Biology]][[Category:Alignment]]
    2 KB (292 words) - 18:36, 12 August 2022
  • Openstructure
    [[Category:Software]][[Category:Biology]] If you like our software and have used it in your research project, please cite the following paper
    3 KB (403 words) - 23:35, 6 February 2023
  • Sputnik
    [[Category:Software]][[Category:Biology]]
    2 KB (311 words) - 15:50, 22 August 2022
  • NCBI C++ Toolkit
    [[Category:Software]][[Category:Biology]][[Category:programming]][[Category:library]][[Category
    3 KB (306 words) - 14:25, 19 August 2022
  • VS Code Remote Development
    * By using the software, you agree to
    7 KB (1,100 words) - 17:42, 5 March 2024
  • TriMetAss
    [[Category:Software]][[Category:Biology]][[Category:NGS]] |{{#vardefine:url|http://microbiology.se/software/trimetass/}}
    3 KB (344 words) - 20:52, 12 August 2022
  • Category:Mapping
    [[Category:Software]]
    8 members (0 subcategories, 0 files) - 17:22, 3 June 2022
  • Cvbio
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (305 words) - 13:11, 21 October 2020
  • Artemis
    [[Category:Software]][[Category:Biology]]
    3 KB (378 words) - 14:53, 12 August 2022
  • Hyb
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]]
    2 KB (247 words) - 15:07, 10 June 2022
  • Spyder
    [[Category:Software]][[Category:Programming]]
    3 KB (350 words) - 18:56, 21 August 2022
  • Nbody
    [[Category:Software]][[Category:Astronomy]] |{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
    2 KB (248 words) - 13:11, 6 June 2022
  • LTRRetriever
    [[Category:Software]][[Category:biology]][[Category:phylogenetics]]
    2 KB (255 words) - 21:21, 6 December 2019
  • RNAhybrid
    [[Category:Software]][[Category:Biology]][[Category:Genomics]]
    2 KB (285 words) - 20:56, 12 August 2022
  • Predector
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (246 words) - 20:21, 31 May 2022
  • Cogent
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (294 words) - 21:06, 6 December 2019
  • Ciriquant
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (275 words) - 15:00, 30 March 2022
  • PICRUSt
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    3 KB (344 words) - 18:28, 10 June 2022
  • MitoPhAST
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (382 words) - 14:27, 23 April 2020
  • Vamb
    [[Category:Software]]
    3 KB (302 words) - 18:59, 1 February 2021
  • KisSplice
    [[Category:Software]][[Category:Biology]] KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It
    3 KB (359 words) - 19:33, 15 August 2022
  • Albacore
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (258 words) - 21:10, 6 December 2019
  • MiRDP2
    [[Category:Software]][[Category:Biology]][[Category:Genomics]]
    3 KB (328 words) - 18:09, 31 May 2022
  • CellRanger-DNA
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]][[Category:Genomic |{{#vardefine:url|https://support.10xgenomics.com/single-cell-dna/software/pipelines/latest/what-is-cell-ranger-dna}}
    2 KB (263 words) - 13:25, 15 August 2022
  • Tuxedo
    [[Category:Software]][[Category:Biology]] See individual software wiki pages for more details.
    598 bytes (81 words) - 20:53, 12 August 2022
  • Numba
    [[Category:Software]][[Category:Compiler]]
    3 KB (353 words) - 20:44, 15 August 2022
  • Squigglenet
    [[Category:Software]][[Category:Sequencing]][[Category:Biology]]
    2 KB (262 words) - 20:12, 9 May 2022
  • RStudio
    [[Category:Software]][[Category:Statistics]]
    3 KB (461 words) - 19:51, 18 July 2023
  • OpenNeuro
    [[Category:Software]][[Category:Data Science]][[Category:Biology]]
    2 KB (248 words) - 17:56, 19 August 2022
  • SibeliaZ
    [[Category:Software]]
    2 KB (284 words) - 20:40, 12 August 2022
  • Circos
    [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]] |{{#vardefine:url|http://circos.ca/software/download/circos/}}
    3 KB (409 words) - 13:35, 15 August 2022
  • Vray
    [[Category:Software]] |{{#vardefine:url|https://www.chaos.com/3d-rendering-software}}
    3 KB (341 words) - 16:46, 6 April 2023
  • AMPtk
    [[Category:Software]][[Category:Biology]][[Category:NGS]]
    2 KB (289 words) - 12:41, 12 August 2022
  • R-index
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (319 words) - 21:24, 6 December 2019
  • Gpufit
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (234 words) - 19:34, 26 May 2022
  • Filtlong
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (299 words) - 21:20, 6 December 2019
  • Category:Molecular Dynamics
    [[Category:Software]]
    16 members (0 subcategories, 0 files) - 15:38, 19 August 2022
  • Lucene
    [[Category:Software]][[Category:Programming]][[Category:Search]]
    2 KB (262 words) - 12:11, 26 August 2022
  • Talk:BioC Requirements Information Gathering
    ...rearely need jobs that run over a month. Between checkpointing and better software, most of the analyses that I've seen running over 30days on our lab cluster
    3 KB (493 words) - 21:42, 2 November 2011
  • 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
  • File:Software.png
    software icon for main menu...possibly
    (500 × 500 (15 KB)) - 13:53, 24 June 2022
  • Corset
    [[Category:Software]][[Category:Biology]][[Category:NGS]] ...gram to go from a de novo transcriptome assembly to gene-level counts. Our software takes a set of reads that have been multi-mapped to the transcriptome (wher
    3 KB (309 words) - 17:09, 10 June 2022
  • DeepGS
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (342 words) - 22:21, 26 August 2020
  • Prottest3
    [[Category:Software]] This software requires GUI. See more: [https://help.rc.ufl.edu/doc/GUI_Programs GUI Progr
    3 KB (369 words) - 15:57, 13 September 2022
  • Starseqr
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (269 words) - 17:12, 31 May 2022
  • KaKs
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]][[Category:Genomics]]
    2 KB (281 words) - 19:18, 15 August 2022
  • Sine scan
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (241 words) - 18:28, 1 June 2022
  • TPMcalculator
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (293 words) - 19:45, 1 June 2022
  • Breakseq
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (247 words) - 21:15, 6 December 2019
  • Yagcloser
    [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:Assembly]]
    2 KB (265 words) - 19:07, 1 April 2024
  • Datamash
    [[Category:Software]][[Category:Math]] |{{#vardefine:url|http://www.gnu.org/software/datamash/}}
    2 KB (247 words) - 15:01, 10 June 2022
  • Graftm
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (322 words) - 22:16, 27 August 2020
  • AlphaFold
    [[Category:Software]][[Category:Phylogenetics]] ...GPU. An example job script for a run with the test data included with the software is shown below.
    6 KB (832 words) - 15:38, 2 February 2024
  • 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
  • PAPI
    [[Category:Software]][[Category:Performance Analysis]][[Category:Programming]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    3 KB (360 words) - 16:36, 21 August 2022
  • Segment-liftover
    [[Category:Software]]
    2 KB (251 words) - 20:38, 12 August 2022
  • Simulia
    [[Category:Software]][[Category:Simulation]][[Category:Visualization]]
    2 KB (252 words) - 18:23, 1 June 2022
  • ESOM
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (242 words) - 15:08, 15 August 2022
  • Category:RNA-Seq
    [[Category:NGS]][[Category:Software]]
    28 members (0 subcategories, 0 files) - 15:28, 23 August 2022
  • Illumiprocessor
    [[Category:Software]][[Category:Phylogenetics]]
    4 KB (452 words) - 18:44, 15 August 2022
  • Mamba
    [[Category:Software]]
    3 KB (429 words) - 20:16, 3 June 2022
  • Biopieces
    [[Category:Software]][[Category:Phylogenetics]] The software requires users to create the BP_DATA, tmp, and BP_LOG directories in your w
    3 KB (410 words) - 15:40, 10 December 2021
  • DeepPicker
    [[Category:Software]][[Category:Imaging]] This software is installed in a container.
    2 KB (281 words) - 14:34, 15 August 2022
  • Sampledock
    [[Category:Software]][[Category:Machine Learning]][[Category:Molecular Dynamics]]
    2 KB (253 words) - 17:59, 15 August 2022
  • PartitionFinder
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]][[Category:Genomics]]
    3 KB (402 words) - 16:57, 21 August 2022
  • NONMEM
    [[Category:Software]][[Category:Modeling]]
    3 KB (439 words) - 21:23, 6 December 2019
  • Olego
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]]
    3 KB (309 words) - 17:44, 19 August 2022
  • Bubbleparse
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (246 words) - 14:43, 10 June 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
  • Aria2
    [[Category:Software]][[Category:Utility]]
    3 KB (326 words) - 14:05, 17 September 2020
  • Cpc
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (287 words) - 17:22, 9 June 2022
  • ADMIXTURE
    [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]] |{{#vardefine:url|https://www.genetics.ucla.edu/software/admixture/index.html}}
    3 KB (366 words) - 20:51, 11 August 2022
  • Gerbil
    [[Category:Software]][[Category:Phylogenetics]] ...hat is specialized for high effiency when counting k-mers for large k. The software is decribed here.
    3 KB (320 words) - 14:34, 3 January 2020
  • Forecasting
    [[Category:Software]]
    3 KB (308 words) - 14:41, 27 January 2023
  • MicrobeAnnotator
    [[Category:Software]][[Category:Annotation]][[Category:Biology]]
    2 KB (270 words) - 19:02, 10 October 2022
  • CoMap
    [[Category:Software]][[Category:Biology]][[Category:Genomics]]
    3 KB (378 words) - 18:39, 12 August 2022
  • DDocent
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (311 words) - 14:29, 15 August 2022
  • Xterm
    [[Category:Software]][[Category:Shell]]
    2 KB (278 words) - 19:37, 11 July 2022
  • Pggb
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (287 words) - 19:56, 6 November 2020
  • Fast5tools
    [[Category:Software]][[Category:Phylogenetics]][[Category:Biology]]
    2 KB (251 words) - 18:31, 28 April 2022
  • TrimAl
    [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:Alignment‏]]
    2 KB (264 words) - 19:32, 24 August 2022
  • PSMC
    [[Category:Software]][[Category:Phylogenetics]] This software package infers population size history from a diploid sequence
    2 KB (263 words) - 14:01, 28 February 2020
  • VARI
    [[Category:Software]][[Category:math]][[Category:visualization]]
    2 KB (248 words) - 14:10, 11 October 2022
  • GrADS
    [[Category:Software]][[Category:Geospatial]][[Category:Math]]
    3 KB (334 words) - 20:26, 24 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
  • DSSP
    [[Category:Software]][[Category:Molecular Dynamics]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    2 KB (297 words) - 19:51, 13 June 2022
  • Minced
    [[Category:Software]][[Category:Biology]][[Category:Genomics]]
    2 KB (263 words) - 15:38, 10 June 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
  • Hapdup
    [[Category:Software]][[Category:Phylogenetics]][[Category:Biology]]
    3 KB (324 words) - 21:07, 7 April 2022
  • PASTA
    [[Category:Software]][[Category:Biology]][[Category:Alignment‏]]
    3 KB (381 words) - 19:31, 24 August 2022
  • Rapidtide
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (281 words) - 13:58, 7 May 2020
  • Simka
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (260 words) - 19:25, 18 February 2021
  • Libunistring
    [[Category:Software]][[Category:Library]] |{{#vardefine:url|https://www.gnu.org/software/libunistring/}}
    2 KB (269 words) - 15:49, 10 June 2022
  • CLIFinder
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    3 KB (308 words) - 21:11, 6 December 2019
  • ImageJ
    [[Category:Software]][[Category:Imaging]]
    2 KB (268 words) - 20:03, 10 June 2022
  • Disbatch
    [[Category:Software]]
    2 KB (246 words) - 15:19, 18 July 2023
  • DEXTRACTOR
    [[Category:Software]][[Category:Biology]][[Category:Sequencing]]
    3 KB (441 words) - 19:20, 10 June 2022
  • Uproc
    [[Category:Software]][[Category:Genomics]][[Category:Biology]]
    3 KB (418 words) - 20:53, 12 August 2022
  • Bamm
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (322 words) - 18:00, 12 August 2022
  • BESST
    [[Category:Software]][[Category:Biology]][[Category:NGS]]
    3 KB (332 words) - 12:51, 15 August 2022
  • Compacta
    [[Category:Software]] Compacta is a software designed to reduce the number of contigs given by
    3 KB (294 words) - 13:52, 15 August 2022
  • AmPEPpy
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (291 words) - 14:13, 22 April 2021
  • HybPiper
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    3 KB (349 words) - 18:36, 10 June 2022
  • Blackfynn
    [[Category:Software]][[Category:Data Mining]]
    2 KB (280 words) - 19:12, 27 May 2022
  • Smudgeplot
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (315 words) - 15:19, 4 May 2021
  • PyBSASeq
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (235 words) - 17:14, 1 June 2022
  • PhyloParser
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (245 words) - 18:17, 21 August 2022
  • Bsmap
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Biology]] BSMAP is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated C
    3 KB (304 words) - 18:22, 12 August 2022
  • SUMO
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (275 words) - 21:24, 6 December 2019
  • Export2graphlan
    export2graphlan is a conversion software tool for producing both
    3 KB (314 words) - 15:12, 15 August 2022
  • LncScore
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    3 KB (308 words) - 21:21, 6 December 2019
  • Ydata-profiling
    [[Category:Software]][[Category:Machine Learning]][[Category:Artificial Intelligence]]
    2 KB (280 words) - 19:05, 1 December 2023
  • Bwa-meth
    [[Category:Software]]
    2 KB (239 words) - 16:59, 24 August 2023
  • Tantan
    [[Category:Software]][[Category:NGS]][[Category:Genomics]]
    2 KB (280 words) - 19:04, 1 June 2022
  • ELPA
    [[Category:Software]][[Category:Math]][[Category:Library]][[Category:Compiler]]
    2 KB (290 words) - 14:58, 15 August 2022
  • Atom
    [[Category:Software]][[Category:Programming]]
    2 KB (273 words) - 15:21, 12 August 2022
  • CRISPRCasFinder
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (288 words) - 21:11, 6 December 2019
  • Phyluce
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]] phyluce (phy-loo-chee) is a software package that was initially developed for analyzing data collected from ultr
    4 KB (517 words) - 18:23, 21 August 2022
  • Caper
    [[Category:Software]][[Category:Data_Science]]
    3 KB (425 words) - 14:43, 11 October 2023
  • Last
    [[Category:Software]][[Category:Biology]][[Category:Alignment]][[Category:Sequencing]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    3 KB (342 words) - 19:29, 12 August 2022
  • Bzip2
    [[Category:Software]][[Category:Utility]][[Category:Library]]
    2 KB (289 words) - 13:16, 15 August 2022
  • DL POLY
    [[Category:Software]][[Category:Molecular Dynamics]] DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith.
    2 KB (309 words) - 17:00, 6 June 2022
  • SimNIBS
    [[Category:Software]][[Category:Phylogenetics]] SimNIBS is a free and open source software package for the Simulation of Non-invasive Brain Stimulation. It allows for
    3 KB (324 words) - 18:04, 28 August 2020
  • Jasmine
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (317 words) - 19:09, 15 August 2022
  • LoFreq
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (244 words) - 21:21, 6 December 2019
  • Z1Plus
    [[Category:Software]]
    2 KB (293 words) - 19:36, 6 September 2023
  • LIBXSMM
    [[Category:Software]][[Category:Library]][[Category:Compiler]][[Category:Math]]
    2 KB (257 words) - 17:46, 15 August 2022
  • Anvio
    [[Category:Software]][[Category:Biology]]
    2 KB (237 words) - 14:20, 12 August 2022
  • Pascal
    [[Category:Software]][[Category:Compiler]][[Category:Programming]]
    3 KB (303 words) - 20:44, 15 August 2022
  • SnpEff
    [[Category:Software]][[Category:Biology]][[Category:Annotation]]
    4 KB (562 words) - 15:19, 5 January 2023
  • Nanocaller
    [[Category:Software]]
    3 KB (351 words) - 15:41, 16 March 2023
  • MetaWRAP
    [[Category:Software]][[Category:Phylogenetics]] ...lexible pipeline for genome-resolved metagenomic data analysis. If certain software wrapped into metaWRAP were integral to your investigation (e.g. Salmon, Max
    3 KB (412 words) - 22:31, 8 September 2020
  • FineRADstructure
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (293 words) - 14:53, 5 January 2022
  • CPLEX
    [[Category:Software]][[Category:Climate]] |{{#vardefine:url|http://www-01.ibm.com/software/commerce/optimization/cplex-optimizer/}}
    2 KB (264 words) - 19:35, 24 August 2022
  • Rapidsai
    [[Category:Software]][[Category:Data Science]] The RAPIDS suite of open source software libraries and APIs gives you the ability to execute end-to-end data science
    3 KB (348 words) - 21:29, 21 August 2022
  • PsiCLASS
    [[Category:Software]][[Category:Phylogenetics]]
    4 KB (480 words) - 15:00, 14 December 2022
  • Ghostscript
    [[Category:Software]][[Category:Documentation]]
    2 KB (254 words) - 17:08, 15 August 2022
  • MRtrix
    [[Category:Software]][[Category:Biology]][[Category:Imaging]] ...Jeurissen, C.-H. Yeh, and A. Connelly. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 202 (
    3 KB (311 words) - 20:34, 24 August 2022
  • IDBA-MT
    [[Category:Software]][[Category:Biology]][[Category:NGS]] ...ased on paired-end RNA sequencing reads only. IDBA-MT is a post-processing software for IDBA-UD contigs for removing chimeria contigs and extending contig leng
    3 KB (315 words) - 21:21, 6 December 2019
  • Regtools
    [[Category:Software]][[Category:Biology]][[Category:RNA-Seq]][[Category:Genomics]]
    2 KB (254 words) - 21:41, 21 August 2022
  • Assemblytics
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (252 words) - 17:02, 29 September 2020
  • Ragout
    [[Category:Software]][[Category:Genomics]]
    3 KB (318 words) - 21:29, 21 August 2022
  • Minimac
    [[Category:Software]][[Category:Biology]][[Category:NGS]]
    3 KB (332 words) - 20:11, 18 August 2022
  • Brewery
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (245 words) - 17:40, 24 January 2020
  • ECE
    [[Category:Software]][[Category:Physics]] Ece software container
    3 KB (360 words) - 21:39, 3 March 2023
  • 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
  • Mutmap
    [[Category:Software]]
    2 KB (236 words) - 16:06, 21 June 2023
  • Canu
    [[Category:Software]][[Category:Biology]][[Category:Sequencing]]
    3 KB (358 words) - 14:26, 14 April 2020
  • Trgt
    [[Category:Software]]
    2 KB (273 words) - 14:45, 28 July 2023
  • Albumentations
    [[Category:Software]][[Category:Machine Learning]][[Category:Imaging]][[Category:Image Processi
    2 KB (263 words) - 12:33, 12 August 2022
  • Nanopolish
    [[Category:Software]][[Category:Biology]]
    2 KB (237 words) - 14:38, 10 June 2022
  • Elastix
    [[Category:Software]][[Category:Phylogenetics]] ...on the well-known Insight Segmentation and Registration Toolkit (ITK). The software consists of a collection of algorithms that are commonly used to solve (med
    3 KB (365 words) - 15:30, 3 June 2022
  • FastqPuri
    [[Category:Software]][[Category:Phylogenetics]] Software and source code of FastqPuri. It creates quality reports of fastq files and
    2 KB (272 words) - 15:29, 19 January 2021
  • Smartie-sv
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (247 words) - 18:30, 1 June 2022
  • MetaGeneMark
    [[Category:Software]][[Category:Biology]][[Category:Genomics]]
    2 KB (298 words) - 21:22, 6 December 2019
  • Gem5
    [[Category:Software]][[Category:Simulation]]
    3 KB (434 words) - 19:23, 10 June 2022
  • PanX
    [[Category:Software]][[Category:Phylogenetics]] panX is a software package for pan-genome analysis, interactive visualization and exploration.
    3 KB (346 words) - 21:22, 6 December 2019
  • Category:Scheduler
    [[Category:Categories]][[Category:Software]]
    18 members (1 subcategory, 0 files) - 15:28, 23 August 2022
  • Category:Material Science
    [[Category:Software]]
    5 members (0 subcategories, 0 files) - 19:53, 22 August 2022
  • Goatools
    [[Category:Software]][[Category:Biology]]
    3 KB (309 words) - 03:26, 2 January 2023
  • Circlator
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (272 words) - 13:34, 15 August 2022
  • Graph-tool
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (285 words) - 17:20, 15 August 2022
  • NewTargets
    [[Category:Software]]
    3 KB (379 words) - 20:06, 12 August 2022
  • ESPRIT
    [[Category:Software]][[Category:Biology]]
    4 KB (460 words) - 15:10, 15 August 2022
  • TreeBreaker
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (271 words) - 21:29, 6 December 2019
  • ClonalFrame
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Phylogenetics]]
    3 KB (349 words) - 18:33, 12 August 2022
  • SQANTI
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (321 words) - 21:24, 6 December 2019
  • TraCeR
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (277 words) - 16:40, 22 August 2022
  • Test
    [[Category:Software]][[Category:shell]]
    2 KB (229 words) - 21:29, 6 December 2019
  • Chromeister
    [[Category:Software]][[Category:Biology]][[Category:Genomics]]
    2 KB (245 words) - 19:42, 23 May 2022
  • Modules
    [[Category:Software]][[Category:Infrastructure]] ...g and maintaining your environment while running a large number of diverse software applications with different requirements can be a daunting task. The Resea
    3 KB (428 words) - 18:21, 7 February 2023
  • Sparsehash
    [[Category:Software]][[Category:web]][[Category:programming]]
    3 KB (322 words) - 18:02, 15 August 2022
  • GFF3toolkit
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (335 words) - 20:48, 23 May 2022
  • ContaVect
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    3 KB (309 words) - 20:40, 10 June 2022
  • COMSOL
    [[Category:Software]][[Category:Simulation]] COMSOL Multiphysics® is a general-purpose simulation software for modeling designs, devices, and processes in all fields of engineering,
    3 KB (426 words) - 19:40, 20 February 2024
  • NPhase
    [[Category:Software]]
    2 KB (275 words) - 17:53, 15 August 2022
  • SExtractor
    [[Category:Software]][[Category:Astronomy]] |{{#vardefine:url|https://www.astromatic.net/software/sextractor}}
    2 KB (281 words) - 21:24, 6 December 2019
  • CNV-Sim
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    3 KB (321 words) - 17:28, 10 June 2022
  • ASHS
    [[Category:Software]][[Category:Biology]][[Category:imaging]] ASHS is a software package for automatic segmentation of hippocampal subfields in MRI scans. A
    3 KB (353 words) - 20:32, 24 August 2022
  • BFAST
    [[Category:Software]][[Category:Biology]][[Category:NGS]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    2 KB (276 words) - 18:16, 12 August 2022
  • Rainbow
    [[Category:Software]][[Category:biology]][[Category:sequencing]]
    2 KB (254 words) - 21:24, 6 December 2019
  • Openmc
    [[Category:Software]]
    2 KB (287 words) - 20:25, 21 February 2024
  • Xroms
    [[Category:Software]]
    2 KB (262 words) - 13:36, 12 January 2024
  • GCT
    [[Category:Software]][[Category:File Management]][[Category:Utility]] The GCT is a nascent effort to provide community-based support for critical software packages for grid computing. The GCT is based on a fork of the Globus Toolk
    2 KB (290 words) - 13:54, 21 October 2022
  • Kalign
    [[Category:Software]]
    2 KB (265 words) - 19:28, 12 August 2022
  • Photutils
    [[Category:Software]][[Category:Astronomy]]
    2 KB (271 words) - 13:11, 6 June 2022
  • Slow5tools
    [[Category:Software]]
    2 KB (259 words) - 17:49, 21 July 2022
  • Fusion twas
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (257 words) - 19:27, 26 May 2022
  • CisGenome
    [[Category:Software]][[Category:Biology]][[Category:Genomics]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    2 KB (249 words) - 18:30, 12 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
  • NMRPipe
    [[Category:Software]][[Category:Biology]] NMRPipe is an extensive software system for processing, analyzing, and exploiting NMR spectroscopic data. An
    3 KB (325 words) - 15:55, 23 August 2022
  • BLUPF90
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] ...ran 90/95 for mixed model computations in animal breeding. The goal of the software is to be as simple as with a matrix package and as efficient as in a progra
    2 KB (275 words) - 16:18, 10 June 2022
  • Wub
    [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]] Tools and software library developed by the ONT Applications group
    2 KB (250 words) - 17:46, 22 August 2022
  • FASTRAL-constrained
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (271 words) - 15:25, 15 August 2022
  • HDF4
    [[Category:Software]][[Category:Library]][[Category:Data Science]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    2 KB (314 words) - 18:16, 15 August 2022
  • Workbench
    [[Category:Software]][[Category:Fluid Dynamics]]
    2 KB (286 words) - 15:34, 19 August 2022
  • CMake
    [[Category:Software]][[Category:Programming]] ...designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configur
    3 KB (326 words) - 13:49, 15 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
  • BLASR
    [[Category:Software]][[Category:Biology]][[Category:NGS]]
    2 KB (236 words) - 18:17, 12 August 2022
  • Glimmer
    [[Category:Software]][[Category:Biology]][[Category:Annotation]] |{{#vardefine:url|https://ccb.jhu.edu/software/glimmer/index.shtml}}
    3 KB (391 words) - 17:09, 15 August 2022
  • PyVCF
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (236 words) - 20:08, 21 August 2022
  • MRIcroGL
    [[Category:Software]][[Category:Biology]][[Category:Imaging]]
    2 KB (294 words) - 20:33, 24 August 2022
  • ClinicaDL
    [[Category:Software]][[Category:Biology]][[Category:imaging]][[Category:Machine Learning]] ...data with deep learning methods. ClinicaDL install includes the 'clinica' software platform for clinical research studies involving patients with neurological
    3 KB (323 words) - 13:41, 15 August 2022
  • OMSV
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (245 words) - 17:49, 19 August 2022
  • Nccl
    [[Category:Software]][[Category:Programming]][[Category:Library]][[Category:GPU]]
    3 KB (293 words) - 20:03, 21 August 2022
  • WebLogo
    [[Category:Software]][[Category:Biology]][[Category:Sequencing]][[Category:Graphics]]
    3 KB (417 words) - 17:40, 22 August 2022
  • NCBI BLAST+
    [[Category:Software]][[Category:biology]]
    3 KB (344 words) - 19:55, 12 August 2022
  • NCL
    [[Category:Software]][[Category:Climate]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    3 KB (329 words) - 20:05, 24 August 2022
  • LIGR
    [[Category:Software]][[Category:Biology]][[Category:Assembly]]
    2 KB (249 words) - 19:55, 15 August 2022
  • Category:Math
    [[Category:Software]]
    64 members (1 subcategory, 0 files) - 21:45, 24 October 2022
  • Cyvcf2
    [[Category:Software]]
    2 KB (260 words) - 14:47, 28 July 2023
  • RMATS-turbo
    [[Category:Software]]
    2 KB (292 words) - 18:14, 8 March 2022
  • Tmux
    [[Category:Software]][[Category:Programming]]
    2 KB (265 words) - 16:38, 22 August 2022
  • YAK
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (293 words) - 16:10, 10 March 2021
  • Dapars
    [[Category:Software]][[Category:Genomics]][[Category:Biology]]
    3 KB (306 words) - 20:05, 23 March 2023
  • 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
  • Delucs
    [[Category:Software]]
    3 KB (301 words) - 14:35, 15 August 2022
  • CLIPSeqTools
    [[Category:Software]][[Category:Biology]][[Category:Sequencing]]
    3 KB (303 words) - 20:30, 10 June 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
  • Consulting
    * Get priority help with software, hardware, coding, or architecture
    2 KB (378 words) - 18:33, 13 June 2023
  • QualiMap
    [[Category:Software]][[Category:Biology]][[Category:Alignment‏]]
    3 KB (326 words) - 19:32, 24 August 2022
  • QuartetScores
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (258 words) - 14:50, 27 April 2020
  • UShER
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (425 words) - 21:08, 13 January 2022
  • Rainbowfish
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (233 words) - 19:18, 2 June 2022
  • IAnnotateSV
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] iAnnotateSV is a Python library and command-line software toolkit to annotate and visualize structural variants detected from Next Ge
    3 KB (330 words) - 21:21, 6 December 2019
  • ATRAM
    [[Category:Software]][[Category:Math]]
    3 KB (350 words) - 15:23, 12 August 2022
  • RDnaTools
    [[Category:Software]][[Category:Phylogenetics]] ...Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol,
    3 KB (361 words) - 21:24, 6 December 2019
  • Trinity
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]][[Category:RNA- |{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
    4 KB (556 words) - 17:10, 22 August 2022
  • Bioawk
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (308 words) - 12:54, 15 August 2022
  • LRBinner
    [[Category:Software]]
    5 KB (527 words) - 14:45, 14 December 2022
  • KIM
    [[Category:Software]][[Category:Simulation]]
    3 KB (322 words) - 19:19, 15 August 2022
  • FastQTL
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (325 words) - 14:40, 22 July 2020
  • Scrappie
    [[Category:Software]]
    3 KB (416 words) - 13:43, 7 April 2021
  • Category:Visualization
    [[Category:Software]][[Category:Data]]
    19 members (0 subcategories, 0 files) - 14:53, 19 August 2022
  • Multimatch-gaze
    [[Category:Software]][[Category:Math]][[Category:Data_Science]]
    3 KB (318 words) - 19:07, 16 May 2023
  • Chimera
    [[Category:Software]][[Category:Biology]][[Category:Modeling]]
    3 KB (296 words) - 18:27, 12 August 2022
  • MitoFinder
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (255 words) - 21:23, 6 December 2019
  • Napari
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (271 words) - 14:23, 19 August 2022
  • Mlcoalsim
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] ...rl|https://bioinformatics.cragenomica.es/numgenomics/people/sebas/software/software.html}}
    3 KB (324 words) - 21:22, 6 December 2019
  • SHRiMP
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Genomics]] SHRiMP is a software package for aligning genomic reads against a target genome. It was primaril
    2 KB (269 words) - 22:55, 21 August 2022
  • WoLFPSort
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (309 words) - 21:29, 6 December 2019
  • Orthologer
    [[Category:Software]][[Category:Biology]] ...e:url|https://www.orthodb.org/orthodb_userguide.html#standalone-orthologer-software}}
    2 KB (238 words) - 20:03, 31 May 2022
  • Asset
    [[Category:Software]]
    2 KB (253 words) - 20:07, 15 June 2023
  • Aquamis
    [[Category:Software]][[Category:Biology]][[Category:Genomics]]
    3 KB (348 words) - 22:07, 20 October 2023
  • P53MH
    [[Category:Software]][[Category:Biology]][[Category:Sequencing]]
    3 KB (344 words) - 18:35, 10 June 2022
  • DeFusion
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (246 words) - 22:22, 26 August 2020
  • Trycycler
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (305 words) - 18:13, 22 July 2021
  • CNSpipeline
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (245 words) - 21:19, 6 December 2019
  • BEDOPS
    [[Category:Software]][[Category:Biology]][[Category:Sequencing]][[Category:NGS]]
    3 KB (317 words) - 12:48, 15 August 2022
  • Moses
    [[Category:Software]]
    3 KB (381 words) - 15:15, 17 October 2022
  • R
    [[Category:Software]][[Category:Statistics]][[Category:Programming]] |{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
    6 KB (981 words) - 20:45, 16 October 2023
  • Pindel
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (279 words) - 21:23, 6 December 2019
  • Tesseract
    [[Category:Software]]
    2 KB (271 words) - 17:29, 3 April 2024
  • BayArea
    [[Category:Software]][[Category:Biology]]
    2 KB (255 words) - 15:02, 10 June 2022
  • GSEA
    [[Category:Software]][[Category:Biology]][[Category:Genomics]] ...://www.pnas.org/content/102/43/15545.abstract To cite your use of the GSEA software, a joint project of UC San Diego and Broad Institute, please reference Subr
    2 KB (298 words) - 17:27, 15 August 2022
  • 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]].
    2,139 members (62 subcategories, 0 files) - 19:53, 20 February 2024
  • DeTiN
    [[Category:Software]][[Category:NGS]][[Category:Genomics]]
    2 KB (249 words) - 14:39, 15 August 2022
  • Ruby
    [[Category:Software]][[Category:Language]][[Category:Programming]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    2 KB (272 words) - 18:55, 21 August 2022
  • SMR
    [[Category:Software]] |{{#vardefine:url|https://cnsgenomics.com/software/smr/#Overview}}
    3 KB (362 words) - 18:27, 19 August 2021
  • MUSCLE
    [[Category:Software]][[Category:Biology]][[Category:Alignment]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    2 KB (313 words) - 19:55, 12 August 2022
  • Plinkseq
    [[Category:Software]][[Category:Biology]][[Category:Library]]
    2 KB (296 words) - 20:25, 12 August 2022
  • Trim Galore
    [[Category:Software]][[Category:Biology]][[Category:NGS]]
    4 KB (512 words) - 20:52, 12 August 2022
  • StringMLST
    [[Category:Software]][[Category:Biology]][[Category:ChIP-Seq]]
    2 KB (292 words) - 20:45, 12 August 2022
  • Mantis
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (368 words) - 17:20, 27 May 2022
  • TaxonKit
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (262 words) - 19:01, 13 December 2021
  • NWChem
    [[Category:Software]][[Category:Chemistry]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    3 KB (379 words) - 13:53, 6 June 2022
  • NetCDF-F
    [[Category:Software]][[Category:Data Science]] |{{#vardefine:url|https://www.unidata.ucar.edu/software/netcdf/}}
    2 KB (269 words) - 16:36, 2 September 2022
  • QIIME
    [[Category:Software]][[Category:Biology]][[Category:genomics]] ...for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily bas
    4 KB (555 words) - 15:15, 19 August 2022
  • Ngstools
    [[Category:Software]][[Category:biology]][[Category:NGS]]
    5 KB (708 words) - 15:31, 14 December 2022
  • BamBam
    [[Category:Software]][[Category:Biology]][[Category:Genomics]] |{{#vardefine:url|http://udall-lab.byu.edu/Research/Software/BamBam.aspx}}
    3 KB (456 words) - 18:00, 12 August 2022
  • LongRanger
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] |{{#vardefine:url|https://support.10xgenomics.com/genome-exome/software/pipelines/latest/installation}}
    2 KB (247 words) - 14:42, 10 June 2022
  • GenotypeHarmonizer
    [[Category:Software]][[Category:Biology]]
    2 KB (286 words) - 19:01, 12 August 2022
  • AnnoTALE
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (326 words) - 14:15, 17 September 2020
  • Freyja
    [[Category:Software]][[Category:Phylogenetics]][[Category:Sequencing]][[Category:Biology]]
    2 KB (289 words) - 16:49, 15 August 2022
  • PAUDA
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Phylogenetics]] |{{#vardefine:url|http://ab.inf.uni-tuebingen.de/software/pauda/}}
    3 KB (367 words) - 17:03, 21 August 2022
  • AlphaMate
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] |{{#vardefine:url|https://alphagenes.roslin.ed.ac.uk/wp/software-2/alphamate/}}
    3 KB (338 words) - 13:46, 9 May 2023
  • QOS Limits
    CPU cores, Memory (RAM), GPU accelerators, software licenses, etc. are referred to as '''Trackable Resources''' (TRES) by the s
    4 KB (598 words) - 03:35, 26 February 2023
  • HYPRE
    [[Category:Software]][[Category:math]]
    2 KB (251 words) - 18:38, 15 August 2022
  • CovNMR
    [[Category:Software]][[Category:Biology]]
    3 KB (350 words) - 15:55, 23 August 2022
  • STAR-Fusion
    [[Category:Software]][[Category:Biology]][[Category:Sequencing]]
    3 KB (306 words) - 16:02, 22 August 2022
  • Sweed
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    2 KB (234 words) - 21:24, 6 December 2019
  • Apptainer
    [[Category:Software]][[Category:Workflow Automation]] or even create a shell in the software environment provided by the container with
    4 KB (609 words) - 16:30, 12 February 2024
  • Pyroms
    [[Category:Software]][[Category:Geospatial]]
    2 KB (287 words) - 20:27, 24 August 2022
  • MuTect
    [[Category:Software]][[Category:Biology]][[Category:Genomics]]
    2 KB (286 words) - 16:33, 10 June 2022
  • Nextstrain
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (295 words) - 14:56, 2 March 2020
  • CONNECT
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (248 words) - 14:53, 24 November 2020
  • PhyML
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
    3 KB (465 words) - 20:22, 12 August 2022
  • MOSAIK
    [[Category:Software]][[Category:Biology]][[Category:Alignment]] |{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
    3 KB (414 words) - 11:59, 19 August 2022
  • Bowtie2
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]] |{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
    3 KB (465 words) - 14:48, 14 December 2022
  • Bsoft
    [[Category:Software]][[Category:Biology]][[Category:Image Processing]] Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in struc
    2 KB (297 words) - 13:14, 15 August 2022
  • Mmaction2
    [[Category:Software]][[Category:Machine Learning]][[Category:Visualization]]
    2 KB (277 words) - 19:16, 6 June 2023
  • MGLTools
    [[Category:Software]] These software tools are highly integrated and based on reusable software
    3 KB (357 words) - 17:03, 6 June 2022
  • VarDictJava
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
    3 KB (334 words) - 17:23, 22 August 2022
  • GHOST-MP
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (285 words) - 20:11, 7 May 2020
  • Nimare
    [[Category:Software]]
    3 KB (343 words) - 15:27, 15 August 2022
  • MetaCluster
    [[Category:Software]][[Category:Biology]][[Category:Genomics]] |{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
    3 KB (321 words) - 19:26, 18 August 2022
  • Gurobi
    [[Category:Software]][[Category:Math]][[Category:Programming]]
    2 KB (269 words) - 12:22, 26 August 2022
  • ITK-SNAP
    [[Category:Software]][[Category:Neuroscience]][[Category:Biology]][[Category:Imaging]] SNAP is a software application used to segment structures in 3D medical images. It provides se
    3 KB (397 words) - 19:23, 12 August 2022
  • HMM-FRAME
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (244 words) - 21:21, 6 December 2019
  • Category:Compression
    [[Category:Software]]
    5 members (0 subcategories, 0 files) - 17:21, 3 June 2022
  • OrthoFiller
    [[Category:Software]][[Category:Phylogenetics]]
    3 KB (306 words) - 20:02, 31 May 2022
  • Bamsnap
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (248 words) - 16:14, 27 May 2022
  • LoRMA
    [[Category:Software]][[Category:Biology]][[Category:NGS]]
    3 KB (301 words) - 14:34, 18 October 2022
  • RagTag
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (263 words) - 15:27, 13 August 2020
  • LoRDEC
    [[Category:Software]][[Category:Phylogenetics]]
    2 KB (258 words) - 13:38, 22 April 2021
  • Orange3
    [[Category:Software]][[Category:Data Mining]] Orange is a component-based data mining software. It includes a range of data visualization, exploration, preprocessing and
    3 KB (309 words) - 17:08, 10 June 2022
  • Braker
    [[Category:Software]][[Category:Phylogenetics]] https://github.com/Gaius-Augustus/BRAKER#citing-braker-and-software-called-by-braker
    2 KB (261 words) - 22:28, 26 August 2020

View (previous 500 | next 500) (20 | 50 | 100 | 250 | 500)

Retrieved from "https://help.rc.ufl.edu/doc/Special:Search"