KSU HPC Software

This is the list of software and libraries available to users of the KSU HPC.  If you don't see a title you are looking for, then just start a service ticket to request it (service@kennesaw.edu or x6999).

    • BEAGLE

      Version: 2.1.2

      This module file will configure your environment to use the BEAGLE libraries on the Kennesaw State HPC Cluster. BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs.

      • Biopython

        Version: 1.68

        This module file will configure your environment to use the Biopython software on the Kennesaw State HPC Cluster. The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. Python is an object oriented, interpreted, flexible language that is becoming increasingly popular for scientific computing. Python is easy to learn, has a very clear syntax and can easily be extended with modules written in C, C++ or FORTRAN. The Biopython web site (http://www.biopython.org) provides an online resource for modules, scripts, and web links for developers of Python-based software for bioinformatics use and research. Basically, the goal of Biopython is to make it as easy as possible to use Python for bioinformatics by creating high-quality, reusable modules and classes. Biopython features include parsers for various Bioinformatics file formats (BLAST, Clustalw, FASTA, Genbank,...), access to online services (NCBI, Expasy,...), interfaces to common and not-so-common programs (Clustalw, DSSP, MSMS...), a standard sequence class, various clustering modules, a KD tree data structure etc. and even documentation.

        • Boost

          Version(s): 1.57.0-gcc, 1.61.0-gcc

          This module file will configure your environment to use the Boost C++ Libraries compiles with GCC on the Kennesaw State HPC Cluster. Boost is a set of libraries for the C++ programming language that provide support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing. It contains over eighty individual libraries. (Wikipedia)

          Version(s): 1.63.0-gcc, 1.63.0-intel

          This module file will configure your environment to use the Boost C++ Libraries compiles with Intel Compilers on the Kennesaw State HPC Cluster. Boost is a set of libraries for the C++ programming language that provide support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing. It contains over eighty individual libraries. (Wikipedia)

          • eigen

            Version(s): 3.2.10, 3.3.1

            Eigen is a high-level C++ library of template headers for linear algebra, matrix and vector operations, geometrical transformations, numerical solvers and related algorithms.

            • gflags

              Version: 2.1.2

              Gflags, the commandline flags library used within Google, differs from other libraries, such as getopt(), in that flag definitions can be scattered around the source code, and not just listed in one place such as main(). In practice, this means that a single source-code file will define and use flags that are meaningful to that file. Any application that links in that file will get the flags, and the gflags library will automatically handle that flag appropriately.

              • glog

                Version: git-b6a5e05

                C++ implementation of the Google logging module.

                • GSL

                  Version: 2.2.1

                  The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite. The complete range of subject areas covered by the library includes: Complex Numbers, Roots of Polynomials, Special Functions, Vectors and Matrices, Permutations, Sorting, BLAS Support, Linear Algebra, Eigensystems, Fast Fourier Transforms, Quadrature, Random Numbers, Quasi-Random Sequences, Random Distributions, Statistics, Histograms, N-Tuples, Monte Carlo Integration, Simulated Annealing, Differential Equations, Interpolation, Numerical Differentiation, Chebyshev Approximation, Series Acceleration, Discrete Hankel Transforms, Root-Finding, Minimization, Least-Squares Fitting, Physical Constants, IEEE Floating-Point, Discrete Wavelet Transforms, Basis splines, Running Statistics, Sparse Matrices, and Linear Algebra Unlike the licenses of proprietary numerical libraries the license of GSL does not restrict scientific cooperation. It allows you to share your programs freely with others.

                  • HDF5

                    Version: 1.10.0p1

                    HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.

                    • HTSlib

                      Version: 1.3.2

                      This module provides the access to the Samtools HTSlib C Library. A C library for reading/writing high-throughput sequencing data.

                      • KIM

                        Version: 1.7.3

                        This module provides the access to OpenKIM via the KIM-API. OpenKIM is an online suite of open source tools for molecular simulation of materials. These tools help to make molecular simulation more accessible and more reliable. Within OpenKIM, you will find an online resource for standardized testing and long-term warehousing of interatomic models and data, and an application programming interface (API) standard for coupling atomistic simulation codes and interatomic potential subroutines.

                        • perl5-libs

                          Version: KSU-01

                          This module file will configure your environment to use some non-standard perl5-libs Libraries on the Kennesaw State HPC Cluster. These are perl5 libraries that other modules may depend on.

                          • ReportLab

                            Version: 3.3.12

                            This module file will configure your environment to use the ReportLab Libraries on the Kennesaw State HPC Cluster. ReportLab is the time-proven, ultra-robust open-source engine for creating complex, data-driven PDF documents and custom vector graphics. It's free, open-source , and written in Python. The package sees 50,000+ downloads per month, is part of standard Linux distributions, is embedded in many products, and was selected to power the print/export feature for Wikipedia.

                            • Voro++

                              Version: 0.4.6

                              This module provides the access to Voro++ via the VORO-API. Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. Voro++ comprises of several C++ classes that can be built as a static library. A command-line utility is also provided that can use most features of the code. The direct cell-by-cell construction makes the library particularly well-suited to handling special boundary conditions and walls. It employs algorithms that are tolerant for numerical precision errors, it exhibits high performance, and it has been successfully employed on very large particle systems.

                              • VTK

                                Version: 7.0.0

                                This module provides the access to the Visualization Toolkit (VTK). The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, modeling, image processing, volume rendering, scientific visualization, and information visualization. VTK also includes ancillary support for 3D interaction widgets, two- and three-dimensional annotation, and parallel computing. At its core, VTK is implemented as a C++ toolkit, requiring users to build applications by combining various objects into an application. The system also supports automated wrapping of the C++ core into Python, Java, and Tcl, so VTK applications may also be written using these interpreted programming languages.

                                • Anaconda2

                                  Version(s): 4.2.0, 4.3.0

                                  Anaconda ("Anaconda Distribution") is a free, easy-to-install package manager, environment manager, Python distribution, and collection of over 720 open source packages with free community support. Anaconda2 is based on Python 2.7.

                                  • Anaconda3

                                    Version: 4.2.0

                                    Anaconda ("Anaconda Distribution") is a free, easy-to-install package manager, environment manager, Python distribution, and collection of over 720 open source packages with free community support. Anaconda3 is based on Python 3.5.

                                    Version: 4.3.0

                                    Anaconda ("Anaconda Distribution") is a free, easy-to-install package manager, environment manager, Python distribution, and collection of over 720 open source packages with free community support. Anaconda3 is based on Python 3.6.

                                     

                                    • Boost.Build

                                      Version(s): 2014.10, 2015.07-git

                                      This module file will configure your environment to use the Boost.Build software on the Kennesaw State HPC Cluster. Boost.Build makes it easy to build C++ projects, everywhere. You name you executables and libraries and list their sources. Boost.Build takes care about compiling your sources with right options, creating static and shared libraries, making executables, and other chores whether you're using gcc, msvc, or a dozen more supported C++ compilers on Windows, OSX, Linux and commercial UNIX systems.

                                      • CMake

                                        Version(s): 3.5.0, 3.6.1, 3.7.1

                                        This module file will configure your environment to run the CMake cross-platform build tools on the Kennesaw State HPC Cluster.

                                        • Gaussian

                                          Version: 09

                                          This module file will configure your environment to run Gaussian on the Kennesaw State HPC Cluster. Gaussian is a program that allows for electronic structure modeling. There are many scientific/modeling features and none impose any limitations on calculations.

                                          • gcc

                                            Version: 6.3.0

                                            This module file will configure your environment to use the gcc compilers on the Kennesaw State HPC Cluster.

                                            • Intel

                                              Version: 17.0.1

                                              This module file will configure your environment to run the Intel C++/Fortran compilers on the Kennesaw State HPC Cluster.

                                              • MATLAB

                                                Version(s): R2015a, R2016a

                                                This module file will configure your environment to run MATLAB on the Kennesaw State HPC Cluster. MATLAB is software for engineers and scientists for analyzing data, developing algorithms, or creating models. MATLAB provides an environment that invites exploration and discovery. It combines a high-level language with a desktop environment tuned for iterative engineering and scientific workflows.

                                                • Python

                                                  Version: 3.5.2

                                                  Python is an interpreted, interactive, object-oriented programming language often compared to Tcl, Perl, Scheme or Java. Python includes modules, classes, exceptions, very high level dynamic data types and dynamic typing. Python supports interfaces to many system calls and libraries, as well as to various windowing systems (X11, Motif, Tk, Mac and MFC). Programmers can write new built-in modules for Python in C or C++. Python can be used as an extension language for applications that need a programmable interface. Python 3 is a new version of the language that is incompatible with the 2.x line of releases. The language is mostly the same, but many details, especially how built-in objects like dictionaries and strings work, have changed considerably, and a lot of deprecated features have finally been removed.

                                                  • R

                                                    Version: 3.3.1

                                                    This module file will configure your environment to use the R software on the Kennesaw State HPC Cluster. R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly ATT, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control.

                                                    • Abinit

                                                      Version: 8.0.8b

                                                      ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties. Excited states can be computed within the Many-Body Perturbation Theory (the GW approximation and the Bethe-Salpeter equation), and Time-Dependent Density Functional Theory (for molecules). In addition to the main ABINIT code, different utility programs are provided.

                                                      • ANNOVAR

                                                        Version: 2016Feb01

                                                        This module file will configure your environment to use the ANNOVAR software on the Kennesaw State HPC Cluster. ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).

                                                        • AtomEye

                                                          Version: 2.2

                                                          AtomEye is an atomistic configuration viewer.

                                                          • AUGUSTUS

                                                            Version: 3.2.3

                                                            This module file will configure your environment to use the AUGUSTUS software on the Kennesaw State HPC Cluster. AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.

                                                            • BamTools

                                                              Version: 2.4.1

                                                              BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

                                                              • BCFtools

                                                                Version: 1.3.1

                                                                This module file will configure your environment to use the BCFtools software on the Kennesaw State HPC Cluster. Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools: Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants NOTE: SAMtools has been split out into the BCFtools and BCFtools packages. You may need to load both modules depending on what you are trying to accomplish.

                                                                • BEDOPS

                                                                  Version: 2.4.20

                                                                  BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.

                                                                  • bedtools

                                                                    Version: 2.26.0

                                                                    Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

                                                                    • bowtie

                                                                      Version: 1.1.2

                                                                      This module file will configure your environment to use the bowtie software on the Kennesaw State HPC Cluster. Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

                                                                      • bowtie2

                                                                        Version: 2.2.9

                                                                        This module file will configure your environment to use the bowtie2 software on the Kennesaw State HPC Cluster. Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

                                                                        • BUSCO

                                                                          Version: 2.0

                                                                          This module file will configure your environment to use the BUSCO software on the Kennesaw State HPC Cluster. BUSCO v2 provides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB v9. BUSCO assessments are implemented in open-source software, with a large selection of lineage-specific sets of Benchmarking Universal Single-Copy Orthologs. These conserved orthologs are ideal candidates for large-scale phylogenomics studies, and the annotated BUSCO gene models built during genome assessments provide a comprehensive gene predictor training set for use as part of genome annotation pipelines.

                                                                          • BWA

                                                                            Version: 0.7.15

                                                                            This module file will configure your environment to use the BWA software on the Kennesaw State HPC Cluster. BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

                                                                             

                                                                            • Canu

                                                                              Version: 1.3

                                                                              Canu provides both a programmer's API and an end-user's toolkit for handling BAM files.

                                                                              • Clustal-Omega

                                                                                Version: 1.2.1

                                                                                This module file will configure your environment to use the Clustal-Omega software on the Kennesaw State HPC Cluster. Clustal-Omega is a general purpose multiple sequence alignment (MSA) program for protein and DNA/RNA. It produces high quality MSAs and is capable of handling data-sets of hundreds of thousands of sequences in reasonable time.

                                                                                • clustalw

                                                                                  Version: 2.1

                                                                                  This module file will configure your environment to use the clustalw software on the Kennesaw State HPC Cluster. Clustal W is a general purpose multiple alignment program for DNA or proteins.

                                                                                  • Cufflinks

                                                                                    Version: 2.2.1

                                                                                    This module file will configure your environment to use the Cufflinks software on the Kennesaw State HPC Cluster. Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.

                                                                                    • DaliLite

                                                                                      Version: 3.3

                                                                                      This module file will configure your environment to use the DaliLite software on the Kennesaw State HPC Cluster.

                                                                                      • ELPH

                                                                                        Version: 1.0.1

                                                                                        This module file will configure your environment to use the ELPH software on the Kennesaw State HPC Cluster.

                                                                                        • EMBOSS

                                                                                          Version: 6.6.0

                                                                                          This module file will configure your environment to use the EMBOSS software on the Kennesaw State HPC Cluster. EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.

                                                                                           

                                                                                          • FAST

                                                                                            Version: 20040222

                                                                                            This module file will configure your environment to use the FAST software on the Kennesaw State HPC Cluster. FAST is a program for aligning three-dimensional protein structures. Given two PDB files, it will compare them and try to establish residue-residue correspondence between the two proteins, so that structural similarity is maximized. Files should be in pdb format.

                                                                                            • FASTA

                                                                                              Version: 36.3.8c

                                                                                              This module file will configure your environment to use the FASTA software on the Kennesaw State HPC Cluster.

                                                                                              • FDist2

                                                                                                Version: 20020705

                                                                                                This module file will configure your environment to use the FDist2 software on the Kennesaw State HPC Cluster. A program to detect loci that might be under selection in samples from structured populations.

                                                                                                • FFmpeg

                                                                                                  Version: 2016Sept06

                                                                                                  This module file will configure your environment to use the FFmpeg software on the Kennesaw State HPC Cluster. FFmpeg is the leading multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play pretty much anything that humans and machines have created. It supports the most obscure ancient formats up to the cutting edge. No matter if they were designed by some standards committee, the community or a corporation. It is also highly portable: FFmpeg compiles, runs, and passes our testing infrastructure FATE across Linux, Mac OS X, Microsoft Windows, the BSDs, Solaris, etc. under a wide variety of build environments, machine architectures, and configurations.

                                                                                                  • FLASH

                                                                                                    Version: 1.2.11

                                                                                                    This module file will configure your environment to use the FLASH software on the Kennesaw State HPC Cluster. FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies.

                                                                                                    • GAMESS

                                                                                                      Version: 18Aug2016

                                                                                                      GAMESS (US) can perform several general computational chemistry calculations, including Hartreeâ€"Fock method, density functional theory (DFT), generalized valence bond (GVB), and multi-configurational self-consistent field (MCSCF). Correlation corrections after these SCF calculations can be estimated by configuration interaction (CI), second order Møllerâ€"Plesset perturbation theory (MP2), and coupled cluster (CC) theory. Solvent effect can be considered using quantum mechanics and molecular mechanics through discrete effective fragment potentials or continuum models (such as PCM). Relativistic corrections can be calculated, including third order Douglas-Kroll scalar terms. While the program does not directly perform molecular mechanics, it can do mixed quantum mechanics and molecular mechanics calculations through effective fragment potentials or through an interface with the Tinker code. The fragment molecular orbital method can be used to treat large systems, by dividing them into fragments. It can also be interfaced with the valence bond VB2000 and XMVB programs and the Natural Bond Orbital (NBO) population analysis program. The input files use a keyword based scheme. For example, $\CONTRL SCFTYP=ROHF MAXIT=30 $ND, which specifies that the SCF part of the code should do an restricted open-shell Hartreeâ€"Fock (ROHF) calculation and quit if the result does not converge in 30 iterations. The output is in an English language text file.

                                                                                                      • Gblocks

                                                                                                        Version: 0.91b

                                                                                                        This module file will configure your environment to use the Gblocks software on the Kennesaw State HPC Cluster. Gblocks is a computer program written in ANSI C language that eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences. These positions may not be homologous or may have been saturated by multiple substitutions and it is convenient to eliminate them prior to phylogenetic analysis. Gblocks selects blocks in a similar way as it is usually done by hand but following a reproducible set of conditions. The selected blocks must fulfill certain requirements with respect to the lack of large segments of contiguous nonconserved positions, lack or low density of gap positions and high conservation of flanking positions, making the final alignment more suitable for phylogenetic analysis. Gblocks outputs several files to visualize the selected blocks. The use of a program such as Gblocks reduces the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible and, finally, facilitates the reproduction of the alignments and subsequent phylogenetic analysis by other researchers. Several parameters can be modified to make the selection of blocks more or less stringent. In general, a relaxed selection of blocks is better for short alignments, whereas a stringent selection is more adequate for longer ones. Be aware that the default options of Gblocks are stringent.

                                                                                                        • Genepop

                                                                                                          Version: 4.5.1

                                                                                                          This module file will configure your environment to use the Genepop software on the Kennesaw State HPC Cluster. GENEPOP is a population genetics software package originally developed by Michel Raymond (Raymond@isem.univ-montp2.fr) and Francois Rousset (Rousset@isem.univ-montp2.fr), at the Laboratiore de Genetique et Environment, Montpellier, France.

                                                                                                          • Glimmer

                                                                                                            Version: 3.02b

                                                                                                            This module file will configure your environment to use the Glimmer software on the Kennesaw State HPC Cluster. Glimmer is a collection of programs for identifying genes in microbial DNA sequences. The system works by creating a variable-length Markov model from a training set of genes and then using that model to attempt to identify all genes in a given DNA sequence.

                                                                                                            • GMAP

                                                                                                              Version: 2016-05-01

                                                                                                              This module file will configure your environment to use the GMAP and GSNAP software on the Kennesaw State HPC Cluster. GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program

                                                                                                              • gnuplot

                                                                                                                Version: 5.0.3

                                                                                                                This module file will configure your environment to use the gnuplot software on the Kennesaw State HPC Cluster. A famous scientific plotting package, features include 2D and 3D plotting, a huge number of output formats, interactive input or script-driven options, and a large set of scripted examples.

                                                                                                                • Grace

                                                                                                                  Version: 5.1.25

                                                                                                                  This module file will configure your environment to use the Grace software on the Kennesaw State HPC Cluster. Grace is a WYSIWYG tool to make two-dimensional plots of numerical data. It runs under various (if not all) flavors of Unix with X11 and M*tif (LessTif or Motif). It also runs under VMS, OS/2, and Windows (95/98/NT/2000/XP). Its capabilities are roughly similar to GUI-based programs like Sigmaplot or Microcal Origin plus script-based tools like Gnuplot or Genplot. Its strength lies in the fact that it combines the convenience of a graphical user interface with the power of a scripting language which enables it to do sophisticated calculations or perform automated tasks.

                                                                                                                  • GROMACS

                                                                                                                    Version: 2016.1

                                                                                                                    This module file will configure your environment to use the GROMACS software on the Kennesaw State HPC Cluster. GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, (check the online reference or manual for details), but there are also quite a few features that make it stand out from the competition.

                                                                                                                    • Gurobi

                                                                                                                      Version: 7.0.1

                                                                                                                      The Gurobi Optimizer is the engine used by over 1400 companies in over two dozen industries to turn data into smarter decisions. It allows users to state their toughest business problems as mathematical models, and then automatically considers billions or even trillions of possible solutions to find the best one. Our solver can be used as both a decision-making assistant, to help guide the choices of a skilled expert, or as a fully automated tool to make decisions with no human intervention. Gurobi has been used to produce measurable improvements in a wide range of high-value business functions, including production, distribution, purchasing, finance, capital investment and human resources. Gurobi has proven itself to be both robust and scalable, and is capable of solving problems involving millions of decision variables. The power of the library is backed by a broad range of intuitive interfaces that make it easy for new users to get up and running quickly, and the best technical support in the industry for when questions come up.

                                                                                                                      • HEASoft

                                                                                                                        Version: 6.19

                                                                                                                        A Unified Release of the FTOOLS and XANADU Software Packages XANADU - High-level, multi-mission tasks for X-ray astronomical spectral, timing, and imaging data analysis FTOOLS - General and mission-specific tools to manipulate FITS files FITSIO Core library responsible for reading and writing FITS files (distributed with FTOOLS) fv - General FITS file browser/editor/plotter with a graphical user interface (distributed with FTOOLS) XSTAR - Tool for calculating the physical conditions and emission spectra of photoionized gases

                                                                                                                        • HH-SUITE

                                                                                                                          Version(s): 2.0.16, 3.0.0, 3.0-beta.1

                                                                                                                          This module file will configure your environment to use the HH-SUITE software on the Kennesaw State HPC Cluster. The HH-suite is an open-source software package for sensitive protein sequence searching. It contains programs that can search for similar protein sequences in protein sequence databases. These sequence searches are a standard tool in modern biology with which the function of unknown proteins can be inferred from their sequence.

                                                                                                                          • HMMER

                                                                                                                            Version: 3.1b2

                                                                                                                            HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). HMMER is often used together with a profile database, such as Pfam or many of the databases that participate in Interpro. But HMMER can also work with query sequences, not just profiles, just like BLAST. For example, you can search a protein query sequence against a database with phmmer, or do an iterative search with jackhmmer. HMMER is designed to detect remote homologs as sensitively as possible, relying on the strength of its underlying probability models. In the past, this strength came at significant computational expense, but as of the new HMMER3 project, HMMER is now essentially as fast as BLAST.

                                                                                                                            • ImageMagick

                                                                                                                              Version: 7.0.3

                                                                                                                              This module file will configure your environment to use the ImageMagick software on the Kennesaw State HPC Cluster. ImageMagick is a software suite to create, edit, compose, or convert bitmap images. It can read and write images in a variety of formats (over 200) including PNG, JPEG, JPEG-2000, GIF, TIFF, DPX, EXR, WebP, Postscript, PDF, and SVG. Use ImageMagick to resize, flip, mirror, rotate, distort, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Ber curves.

                                                                                                                              • I-TASSER

                                                                                                                                Version(s): 4.4, 5.0

                                                                                                                                This module file will configure your environment to use the I-TASSER software on the Kennesaw State HPC Cluster. I-TASSER is an integrated package for protein structure and function predictions. For a given sequence, I-TASSER first identifies template proteins from the Protein Data Bank (PDB) by multiple threading techniques (LOMETS). The continuous fragments excised from the template alignments are used to assemble full-length models by iterative Monte Carlo simulations. The best models are then selected from the Monte Carlo trajectories by decoy clustering. The final atomic models are rebuilt from the structure clusters by atomic-level structural refinements. An alias (runI-TASSER) is included that automatically enters the -pkgdir, -libdir, and -java_home options for you.

                                                                                                                                • Jellyfish

                                                                                                                                  Version: 2.2.6

                                                                                                                                  Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the "jellyfish dump" command, or queried for specific k-mers with "jellyfish query". See the UserGuide provided on Jellyfish's home page for more details. If you use Jellyfish in your research, please cite: Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics (2011) 27(6): 764-770 (first published online January 7, 2011) doi:10.1093/bioinformatics/btr011

                                                                                                                                  • LAMMPS

                                                                                                                                    Version(s): 17Nov16, 30Jul16

                                                                                                                                    This module file will configure your environment to use the LAMMPS software on the Kennesaw State HPC Cluster. LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using a variety of force fields and boundary conditions.

                                                                                                                                    Version: 30Jul16-icc

                                                                                                                                    This module file will configure your environment to use the LAMMPS software on the Kennesaw State HPC Cluster. LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using a variety of force fields and boundary conditions. This version was built with Intel's compilers to possibly boost performance.

                                                                                                                                    • lp_solve

                                                                                                                                      Version: 5.5.2.5

                                                                                                                                      This module file will configure your environment to use the lp_solve software on the Kennesaw State HPC Cluster. lp_solve is a Mixed Integer Linear Programming (MILP) solver.

                                                                                                                                      • luscus

                                                                                                                                        Version: 0.8.1

                                                                                                                                        This module file will configure your environment to use the luscus software on the Kennesaw State HPC Cluster. Luscus is the program for graphical display and editing of molecular systems. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus can also visualize dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to point out a geometrical feature or a physical quantity. The program is developed as a graphical interface for MOLCAS program package, however it's adaptive nature makes possible using luscus with other computational program packages and chemical formats. If you use this program, please cite: G. Kovaevi, V. Veryazov, J. Cheminformatics, 7 (2015) 1-10; DOI: 10.1186/s13321-015-0060-z

                                                                                                                                        • MAFFT

                                                                                                                                          Version: 7.222

                                                                                                                                          This module file will configure your environment to use the MAFFT software on the Kennesaw State HPC Cluster. Multiple sequence alignment (MSA) plays an important role in evolutionary analyses of biological sequences. MAFFT is an MSA program, first released in 2002, because of its high performance MAFFT is becoming popular in recent years. Multiple sequence alignment (MSA) plays an important role in evolutionary analyses of biological sequences. MAFFT is an MSA program, first released in 2002, because of its high performance MAFFT is becoming popular in recent years.

                                                                                                                                          Version(s): 7.273, 7.294

                                                                                                                                          This module file will configure your environment to use the MAFFT software on the Kennesaw State HPC Cluster. This version uses at most x2 memory space in comparison with previous versions. If it stops due to memory shortage, try version 7.222. Multiple sequence alignment (MSA) plays an important role in evolutionary analyses of biological sequences. MAFFT is an MSA program, first released in 2002, because of its high performance MAFFT is becoming popular in recent years.

                                                                                                                                          • Modeller

                                                                                                                                            Version: 9.16

                                                                                                                                            This module file will configure your environment to use the Modeller software on the Kennesaw State HPC Cluster. Modeller is most frequently used for homology or comparative protein structure modeling: The user provides an alignment of a sequence to be modeled with known related structures and Modeller will automatically calculate a model with all non-hydrogen atoms (these structures are often homologs, but certainly don't have to be, hence the term comparative modeling).

                                                                                                                                            • Molcas@UU

                                                                                                                                              Version: 8.0.15-06-18

                                                                                                                                              This module file will configure your environment to use the Molcas@UU software on the Kennesaw State HPC Cluster. Molcas is a quantum chemistry software developed by scientists to be used by scientists. The basic philosophy behind MOLCAS is to develop methods that will allow an accurate ab initio treatment of very general electronic structure problems for molecular systems in both ground and excited states.

                                                                                                                                               

                                                                                                                                              • Molden

                                                                                                                                                Version: 5.7

                                                                                                                                                This module file will configure your environment to use the Molden software on the Kennesaw State HPC Cluster. Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format. Molden reads all the required information from the GAMESS / GAUSSIAN outputfile. Molden is capable of displaying Molecular Orbitals, the electron density and the Molecular minus Atomic density.

                                                                                                                                                • mothur

                                                                                                                                                  Version: 1.37.4

                                                                                                                                                  This module file will configure your environment to use the mothur software on the Kennesaw State HPC Cluster. The mothur project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. We have incorporated the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more. In addition to improving the flexibility of these algorithms, we have added a number of other features including calculators and visualization tools.

                                                                                                                                                  • MrBayes

                                                                                                                                                    Version: 3.2.6

                                                                                                                                                    This module file will configure your environment to use the MrBayes software on the Kennesaw State HPC Cluster. MrBayes 3 is a program for Bayesian inference and model choice across a large space of phylogenetic and evolutionary models.

                                                                                                                                                    • MToolBox

                                                                                                                                                      Version: 0.3.3

                                                                                                                                                      This module file will configure your environment to use the MToolBox software on the Kennesaw State HPC Cluster. MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome variability and disease-associations for mitochondrial variants. MToolBox provides also a Variant Call Format file (version 4.0) featuring, for the first time, allele-specific heteroplasmy.

                                                                                                                                                      • MT-Toolbox

                                                                                                                                                        Version: 4.1.2

                                                                                                                                                        This module file will configure your environment to use the MT-Toolbox software on the Kennesaw State HPC Cluster. MT-Toolbox is a user friendly software package for analysis of molecule tagged Illumina MiSeq reads. Molecule tagging is a molecular biology technique to significantly reduce amplicon sequence error and PCR bias which can be applied to any amplicon sequencing project. MT-Toolbox converts raw reads into high quality consensus sequences based on each reads molecule tag. For details and other important information please refer to the MT-Toolbox webpage

                                                                                                                                                        • MUSCLE

                                                                                                                                                          Version(s): 3.8.1551, 3.8.31

                                                                                                                                                          This module file will configure your environment to use the MUSCLE software on the Kennesaw State HPC Cluster. MUSCLE enables high-throughput applications to achieve average accuracy comparable to the most accurate tools previously available, which we expect to be increasingly important in view of the continuing rapid growth in sequence data.

                                                                                                                                                          • NCBI-Blast

                                                                                                                                                            Version(s): 2.3.0+

                                                                                                                                                            This module file will configure your environment to use the NCBI-Blast+ software on the Kennesaw State HPC Cluster. The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. There are versions of BLAST that compare protein queries to protein databases, nucleotide queries to nucleotide databases, as well as versions that translate nucleotide queries or databases in all six frames and compare to protein databases or queries.

                                                                                                                                                            • ParaView

                                                                                                                                                              Version: 5.2.0

                                                                                                                                                              This module file will configure your environment to use the ParaView software on the Kennesaw State HPC Cluster. ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView http://www.paraview.org/ batch processing capabilities. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of petascale size as well as on laptops for smaller data, has become an integral tool in many national laboratories, universities and industry, and has won several awards related to high performance computation.

                                                                                                                                                              • PHYLIP

                                                                                                                                                                Version: 3.696

                                                                                                                                                                This module file will configure your environment to use the PHYLIP libraries on the Kennesaw State HPC Cluster.

                                                                                                                                                                • PhyML

                                                                                                                                                                  Version: 3.1

                                                                                                                                                                  This module file will configure your environment to use the PhyML software on the Kennesaw State HPC Cluster. PHYLIP, the Phylogeny Inference Package, is a package of programs for inferring phylogenies (evolutionary trees). It has been distributed since 1980, and has over 30,000 registered users, making it the most widely distributed package of phylogeny programs. Input files in text only format.

                                                                                                                                                                  • primer3

                                                                                                                                                                    Version: 2.3.7

                                                                                                                                                                    This module file will configure your environment to use the primer3 software on the Kennesaw State HPC Cluster. Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers. PCR is used for many different goals. Consequently, primer3 has many different input parameters that you control and that tell primer3 exactly what characteristics make good primers for your goals.

                                                                                                                                                                    • PROBCONS

                                                                                                                                                                      Version: 1.12

                                                                                                                                                                      This module file will configure your environment to use the PROBCONS software on the Kennesaw State HPC Cluster. The basis for the PROBCONS algorithm is the computation of pairwise posterior probability matrices, P(xi ~ yj | x, y), which give the probability that one should match letters xi and yj when aligning two sequences x and y. PROBCONS uses a simple probabilistic model that allows for efficient computation of these probabilities. Given these posterior matrices, PROBCONS applies the probabilistic consistency transformation to incorporate evidence from intermediate sequences. Finally, PROBCONS performs progressive alignment using a sum-of-pairs maximum expected accuracy objective function. Because of the algorithm Probcons is best suited for a smaller number of sequences >1000. When getting over this number the amount of time needed for alignment can be drastically increased.

                                                                                                                                                                      • PROMALS

                                                                                                                                                                        Version: 3D

                                                                                                                                                                        This module file will configure your environment to use the PROMALS software on the Kennesaw State HPC Cluster. PROMALS3D (PROfile Multiple Alignment with predicted Local Structures and 3D constraints) is a tool for aligning multiple protein sequences and/or structures, with enhanced information from database searches, secondary structure prediction, 3D structures or user-defined constraints.

                                                                                                                                                                        • ProtTest

                                                                                                                                                                          Version: 3.4.2

                                                                                                                                                                          This module file will configure your environment to use the ProtTest software on the Kennesaw State HPC Cluster. ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand. ProtTest makes this selection by finding the model in the candidate list with the smallest Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT). At the same time, ProtTest obtains model-averaged estimates of different parameters (including a model-averaged phylogenetic tree) and calculates their importance(Posada and Buckley 2004). ProtTest differs from its nucleotide analog jModeltest (Posada 2008) in that it does not include likelihood ratio tests, as not all models included in ProtTest are nested. ProtTest is written in Java and uses the program PhyML (Guindon and Gascuel, 2003) for the maximum likelihood (ML) estimation of phylogenetic trees and model parameters. The current version of ProtTest (3.2) includes 15 different rate matrices that result in 120 different models when we consider rate variation among sites (+I: invariable sites; +G: gamma-distributed rates) and the observed amino acid frequencies (+F).

                                                                                                                                                                          • PyMol

                                                                                                                                                                            Version: 1.8.2.1

                                                                                                                                                                            This module file will configure your environment to use the PyMol software on the Kennesaw State HPC Cluster. PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating 3D molecular structures.

                                                                                                                                                                            • qhost

                                                                                                                                                                              Version: 1.3.1

                                                                                                                                                                              This module file will configure your environment to use the QHost software on the Kennesaw State HPC Cluster. Gridengine qhost replacement for PBS based systems. Summarize pbsnodes output in a quick list. View execution node information such as processors, running jobs, memory stats, and state. Add something here later, maybe...

                                                                                                                                                                              • Salmon

                                                                                                                                                                                Version: 0.7.2

                                                                                                                                                                                Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves is accuracy and speed via a number of different innovations, including the use of quasi-mapping (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference. The result is a versatile tool that fits nicely into many differnt pipelines. For example, you can choose to make use of our quasi-mapping algorithm by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. an unsorted BAM file produced with your favorite aligner), and it will use the same wicked-fast, state-of-the-art inference algorithm to estimate transcript-level abundances for your experiment. NOTE: Salmon works by (quasi)-mapping sequencing reads directly to the transcriptome. This means the Salmon index should be built on a set of target transcripts, not on the genome of the underlying organism. If indexing appears to be taking a very long time, or using a tremendous amount of memory (which it should not), please ensure that you are not attempting to build an index on the genome of your organism!

                                                                                                                                                                                • SAMtools

                                                                                                                                                                                  Version: 0.1.19

                                                                                                                                                                                  This module file will configure your environment to use the SAMtools and BCFtools software on the Kennesaw State HPC Cluster. Samtools is a suite of programs for interacting with high-throughput sequencing data. It is composed of two parts: SAMtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format BCFtools: Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants

                                                                                                                                                                                  Version: 1.3.1

                                                                                                                                                                                  This module file will configure your environment to use the SAMtools software on the Kennesaw State HPC Cluster. Samtools is a suite of programs for interacting with high-throughput sequencing data. SAMtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format NOTE: SAMtools has been split out into the SAMtools and BCFtools packages. You may need to load both modules depending on what you are trying to accomplish.

                                                                                                                                                                                  • SeaView

                                                                                                                                                                                    Version: 4.6.1

                                                                                                                                                                                    This module file will configure your environment to use the SeaView software on the Kennesaw State HPC Cluster. SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. o SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees. o SeaView drives programs muscle or Clustal Omega for multiple sequence alignment, and also allows to use any external alignment algorithm able to read and write FASTA-formatted files. o Seaview drives the SeaView program to select blocks of evolutionarily conserved sites. o SeaView computes phylogenetic trees by o parsimony, using PHYLIP's dnapars/protpars algorithm, o distance, with NJ or BioNJ algorithms on a variety of evolutionary distances, o maximum likelihood, driving program PhyML 3.1. o SeaView prints and draws phylogenetic trees on screen, SVG, PDF or PostScript files. o SeaView allows to download sequences from EMBL/GenBank/UniProt using the Internet.

                                                                                                                                                                                    • Simcoal2

                                                                                                                                                                                      Version: 2.1.2

                                                                                                                                                                                      This module file will configure your environment to use the Simcoal2 software on the Kennesaw State HPC Cluster. A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models.

                                                                                                                                                                                      • Template

                                                                                                                                                                                        Version: 1.0.0

                                                                                                                                                                                        This module file will configure your environment to use the TEMPLATE software on the Kennesaw State HPC Cluster. This is some descriptive text that is probably borrowed from the software project web site. Try not to pick anything that refers to Windows or cost...

                                                                                                                                                                                        • TeXLive

                                                                                                                                                                                          Version: 2016

                                                                                                                                                                                          This module file will configure your environment to use the TeXLive software on the Kennesaw State HPC Cluster. TeXLive is an easy way to get up and running with the TeX document production system. It provides a comprehensive TeX system with binaries for most flavors of Unix, including GNU/Linux, and also Windows. It includes all the major TeX-related programs, macro packages, and fonts that are free software, including support for many languages around the world.

                                                                                                                                                                                          • TopHat

                                                                                                                                                                                            Version: 2.1.1

                                                                                                                                                                                            This module file will configure your environment to use the TopHat software on the Kennesaw State HPC Cluster. TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

                                                                                                                                                                                            • Trinity

                                                                                                                                                                                              Version(s): 2.1.1, 2.2.0

                                                                                                                                                                                              This module file will configure your environment to use the Trinity software on the Kennesaw State HPC Cluster. Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads.

                                                                                                                                                                                              • VCFtools

                                                                                                                                                                                                Version: 490848f

                                                                                                                                                                                                This module file will configure your environment to use the VCFtools software on the Kennesaw State HPC Cluster. VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project (http://www.1000genomes.org/). The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. This toolset can be used to perform the following operations on VCF files:
                                                                                                                                                                                                * Filter out specific variants
                                                                                                                                                                                                * Compare files
                                                                                                                                                                                                * Summarize variants
                                                                                                                                                                                                * Convert to different file types
                                                                                                                                                                                                * Validate and merge files
                                                                                                                                                                                                * Create intersections and subsets of variants VCFtools consists of two parts, a perl module and a binary executable. The perl module is a general Perl API for manipulating VCF files, whereas the binary executable provides general analysis routines

                                                                                                                                                                                                • Velvet

                                                                                                                                                                                                  Version: 1.2.10

                                                                                                                                                                                                  This module file will configure your environment to use the Velvet software on the Kennesaw State HPC Cluster. Velvet is a sequence assembler for very short reads.

                                                                                                                                                                                                  Version: 1.2.10-maxk63-big

                                                                                                                                                                                                  This module file will configure your environment to use the Velvet software on the Kennesaw State HPC Cluster. Velvet is a sequence assembler for very short reads. This version supports multithreading, big assemblies (more the 2.2 billion reads), and hash-lengths of up to 63bp.

                                                                                                                                                                                                  Version: 1.2.10-maxk63-categ14-big

                                                                                                                                                                                                  This module file will configure your environment to use the Velvet software on the Kennesaw State HPC Cluster. Velvet is a sequence assembler for very short reads. This version supports multithreading, big assemblies (more than 2.2 billion reads), 14 channels, and hash-lengths of up to 63bp.

                                                                                                                                                                                                  • VMD

                                                                                                                                                                                                    Version: 1.9.2

                                                                                                                                                                                                    This module file will configure your environment to use the VMD software on the Kennesaw State HPC Cluster. VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

                                                                                                                                                                                                    • Wise2

                                                                                                                                                                                                      Version: 2.4.1

                                                                                                                                                                                                      This module file will configure your environment to use the Wise2 software on the Kennesaw State HPC Cluster. The Wise2 package is now a rather stately bioinformatics package that has be around for a while. Its key programs are genewise, a program for aligning proteins or protein HMMs to DNA, and dynamite a rather cranky "macro language" which automates the production of dynamic programming.

                                                                                                                                                                                                      • Xmakemol

                                                                                                                                                                                                        Version: 5.16

                                                                                                                                                                                                        This module file will configure your environment to use the Xmakemol software on the Kennesaw State HPC Cluster. XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds.

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