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| |<span style="color:green">GATK4</span> | | |<span style="color:red">GAP 4.11</span> |
| |<span style="color:green">In Progress</span> | | |<span style="color:red">In Progress</span> |
| |<span style="color:green">Oct 2018</span> | | |<span style="color:red">June 2021</span> |
| |<span style="color:green">Oct 2018</span>
| | |<span style="color:red">July 2021</span> |
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| | |<span style="color:red">Stalled due to issues with dependent packages</span> |
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| |<span style="color:green">GffCompare v0.10.5</span>
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| |<span style="color:green">Under Review</span> | |
| |<span style="color:green">Oct 2018</span> | |
| |<span style="color:green">Oct 2018</span>
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| |<span style="color:blue">HMMER v3.2.1</span> | | |<span style="color:green">Intel OneAPI Toolkit 2021</span> |
| |<span style="color:green">In Progress</span> | | |<span style="color:green">In Progress</span> |
| |<span style="color:green">Oct 2018</span> | | |<span style="color:green">June 2021</span> |
| |<span style="color:green">Oct 2018</span> | | |<span style="color:green">July 2021</span> |
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| |<span style="color:blue">HTSeq v0.10.0</span> | | |<span style="color:green">Haddock 2.4</span> |
| |<span style="color:green">In Progress</span> | | |<span style="color:green">In Progress</span> |
| |<span style="color:green">Oct 2018</span> | | |<span style="color:green">June 2021</span> |
| |<span style="color:green">Oct 2018</span> | | |<span style="color:green">July 2021</span> |
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| |<span style="color:blue">METAL r2018-08-28</span> | | |<span style="color:blue">Amber20/AmberTools2020</span> |
| |<span style="color:green">In Progress</span>
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| |<span style="color:green">Oct 2018</span>
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| |<span style="color:green">Oct 2018</span>
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| |<span style="color:blue">Schrodinger Suite 2018</span>
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| |<span style="color:green">In Progress</span>
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| |<span style="color:green">Oct 2018</span>
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| |<span style="color:green">Oct 2018</span>
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| |<span style="color:blue">NCBI-VDB v2.9.3</span>
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| |<span style="color:blue">Pending</span> | | |<span style="color:blue">Pending</span> |
| |<span style="color:blue">Oct 2018</span> | | |<span style="color:blue">July 2021</span> |
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| |<span style="color:blue">PLINK v2.0</span> | | |<span style="color:blue">GNUplot 5.4</span> |
| |<span style="color:blue">Pending</span> | | |<span style="color:blue">Pending</span> |
| |<span style="color:blue">Oct 2018</span> | | |<span style="color:blue">July 2021</span> |
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| |<span style="color:blue">SURPI 1.0.18</span> | | |<span style="color:blue">MuTect</span> |
| |<span style="color:blue">Pending</span> | | |<span style="color:blue">Pending</span> |
| |<span style="color:blue">Nov 2018</span> | | |<span style="color:blue">July 2021</span> |
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| |<span style="color:blue">Trinotate 2.0.0</span> | | |<span style="color:blue">Mummer</span> |
| |<span style="color:blue">Pending</span> | | |<span style="color:blue">Pending</span> |
| |<span style="color:blue">Nov 2018</span> | | |<span style="color:blue">July 2021</span> |
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| |<span style="color:blue">LAMMPS 22Aug2018</span> | | |<span style="color:blue">Psi4 1.3.2</span> |
| |<span style="color:blue">Pending</span> | | |<span style="color:blue">Pending</span> |
| |<span style="color:blue">Nov 2018</span> | | |<span style="color:blue">Aug 2021</span> |
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| |}
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| | |
| = Recently Completed Software Projects =
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| {| class=wikitable
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| |- style="background-color:#f1edbe;"
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| |'''Application Name'''
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| |'''Date Completed'''
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| |'''License Type'''
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| |'''Notes'''
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| |'''Additional Info'''
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| |RepeatMasker 4.0.7
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| |10/19/2018
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| |Open Source
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| |-
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| |MEME 5.0.2
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| |10/16/2018
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| |Open Source
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| |-
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| |[[Matlab|Matlab R2018b]]
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| |10/12/2018
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| |USF Site License
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| |-
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| |STAR 2.6.0a
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| |10/11/2018
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| |Open Source
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| |-
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| |Cell Ranger 2.1.0
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| |10/08/2018
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| |Open Source
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| |-
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| |RUST 1.29.1
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| |10/05/2018
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| |Open Source
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| |-
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| |Go Programming Language 1.11.1
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| |10/05/2018
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| |Open Source
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| |-
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| |IBM CPLEX Optimization Studio 12.8
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| |10/05/2018
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| |Academic License
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| |-
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| |CellProfiler 3.1.5
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| |10/02/2018
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| |Open Source
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| |-
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| |BEDOPS 2.4.35
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| |10/01/2018
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| |Open Source
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| |BEAST 1.10.1
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| |09/27/2018
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| |Open Source
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| |-
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| |AdapterRemoval 2.1.7
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| |09/27/2018
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| |Open Source
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| |-
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| |LiftOver 2018-0918
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| |09/26/2018
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| |Open Source
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| |-
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| |Kallisto 0.44.0
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| |09/24/2018
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| |Open Source
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| |IGV 2.4.14
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| |09/21/2018
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| |Open Source
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| |[[MAGMA|MAGMA 2.24-1]]
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| |09/17/2018
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| |Restricted - Authorized users only
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| |FLINT 2.5.2
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| |09/07/2018
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| |Open Source
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| |-
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| |MPFR 4.0.1
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| |09/06/2018
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| |Open Source
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| |MPIR 3.0.0
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| |09/05/2018
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| |Open Source
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| |-
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| |YASM 1.3.0
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| |09/04/2018
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| |Open Source
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| |-
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| |OrthoFinder 2.2.7
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| |08/30/2018
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| |Open Source
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| |Updated to recently released 2.2.7 and integrated with 9 additional dependencies.
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| |[[Maple|Maple 2018]]
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| |08/17/2018
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| |USF Site License
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| |[[Mothur|Mothur 1.40.5]]
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| |07/31/2018
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| |Open Source
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| |GISMO 1.1.0
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| |07/26/2018
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| |Open Source
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| |Matlab add-on package for seismic data analysis
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| |Installed and available in /apps/matlab/share/GISMO on the CIRCE cluster.
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| |-
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| |[[Development_Tools|Perl 5.28.0]]
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| |07/12/2018
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| |Open Source
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| |Newer version of Perl programming language needed for some applications.
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| |[[SCIP|SCIP 6.0.0]]
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| |07/02/2018
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| |Open Source
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| |Dependency issues prevented 5.X versions from installing properly. A work-around was developed and found to be valid with the 6.0.0 version.
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| |Contact rc-help@usf.edu for details regarding work-around if SCIP > 3.1.1 is needed.
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| |[[ANSYS_EDT_(formerly_HFSS)|Ansys Electronics Desktop Suite v19.1]]
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| |06/29/2018
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| |Restricted - Authorized users only
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| |Electromagnetic and circuit design applications including HFSS, Maxwell, etc.
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| |[[ANSYS|Ansys Multiphysics v19.1]]
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| |06/29/2018
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| |Restricted - Authorized users only
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| |ANSYS finite-element analysis applications
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| |[[Wannier90|Wannier90 2.1.0]]
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| |06/29/2018
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| |Open Source
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| |[[Quantum_Espresso|Quantum Espresso 6.2.1]]
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| |06/28/2018
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| |Open Source
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| |-
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| |[[MaxQuant|MaxQuant 1.6.2.3]]
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| |06/15/2018
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| |Academic License
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| |Required an update of system tool "mono" to the specific version 5.4.1.7
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| |[[Blast|NCBI Blast 2.7.1+]]
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| |06/07/2018
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| |Open Source
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| |Issues encountered and resolved when compiling on RHEL6 using Intel compilers
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| |Standalone and dependency for OrthoFinder
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| |-
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| |Circos 0.69-6
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| |06/06/2018
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| |Open Source
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| |Requires additional Perl modules for full functionality and an update to Perl 5.27
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| |-
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| |LinBox 1.5.2
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| |05/22/2018
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| |Open Source
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| |Required updated install of 8 additional library packages
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| |-
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| |MPlus 8
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| |05/15/2018
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| |Restricted - Authorized users only
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| |-
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| |[[Matlab|Matlab R2018a]]
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| |05/14/2018
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| |USF Site License
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| |
| |
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| |-
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| |[[Mathematica|Mathematica 11.3]]
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| |05/11/2018
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| |USF Site License
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| |
| |
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| |-
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| |[[Julia|Julia 0.6.2]]
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| |05/03/2018
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| |Open Source
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| |[[R_and_Rmpi|R 3.5.0]]
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| |04/30/2017
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| |Open Source
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| |-
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| |RSEM 1.3.0
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| |04/27/2018
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| |Open Source
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| |-
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| |Tophat 2.1.1
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| |04/26/2018
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| |Open Source
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| |-
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| |Pear 0.9.11
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| |04/20/2018
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| |Open Source
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| |-
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| |[[Bowtie2|Bowtie 2.3.4.1]]
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| |04/19/2018
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| |Open Source
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| |-
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| |Intel Parallel Studio XE 2018
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| |04/18/2018
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| |USF Site License
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| |
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| |-
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| |Trimmomatic 0.36
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| |04/12/2018
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| |Open Source
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| |-
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| |[[SIESTA|SIESTA 4.0.1]]
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| |04/05/2018
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| |Open Source
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| |-
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| |[[SPAdes|SPAdes 3.11.1]]
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| |03/30/2018
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| |Open Source
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| |-
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| |Psi4 1.1
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| |03/15/2018
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| |Open Source
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| |-
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| |[[Development_Tools|GCC 7.3.0]]
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| |02/28/2018
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| |GNU License
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| |
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| |-
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| |[[Development_Tools|OpenMPI 2.0.4]]
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| |03/14/2018
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| |GNU License
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| |-
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| |[[COMSOL|COMSOL 5.3a]]
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| |02/28/2018
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| |USF Site License
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| |-
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| |[[Trinity|Trinity 2.6.5]]
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| |02/26/2018
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| |Open Source
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| |-
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| |[[SageMath|SageMath 7.5.1]]
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| |02/12/2018
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| |Open Source
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| |-
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| |[[Cufflinks|Cufflinks 2.2.1]]
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| |02/07/2018
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| |Open Source
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| |-
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| |[[ORCA|ORCA 4.0.1]]
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| |02/05/2018
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| |Open Source
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| |-
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| |[[SPECFEM3D|SPECFEM3D 3.0]]
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| |01/30/2018
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| |Open Source
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| |-
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| |[[MEGA|MEGA-CC 7.0.26-1]]
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| |01/08/2018
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| |Open Source
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| |-
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| |[[MUSCLE|MUSCLE 3.8.31]]
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| |01/08/2018
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| |Open Source
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