Software Available On The HPC

Module Version Default Category Description
Anaconda2 4.2.0
4.3.0
5.3.0
2018.12
4.3.0 Programming 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 4.2.0
4.3.0
4.4.0
5.3.0
2018.12
4.3.0 Programming 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.
Bazel 0.4.5
0.11.0
0.18.0
0.4.5 Programming Bazel is a build tool which coordinates builds and run tests. It works with source files written in any language, with native support for Java, C, C++ and Python. Bazel produces builds and runs tests for multiple platforms.
Boost.Build 2014.10
2015.07-git
2014.10 Programming 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 3.5.0
3.6.1
3.7.1
3.8.1
3.12.4
3.12.4 Programming
Eclipse 4.6
4.8
4.8 Programming
Gaussian 09
16
16_B01
16 Programming Gaussian is a program that allows for electronic structure modeling. There are many scientific/modeling features and none impose any limitations on calculations.  This environment module attempts to load the most appropriate version of Gaussian and Linda based on CPU capabilities.
gcc 6.3.0
8.2.0
8.2.0 Programming The GNU Compiler Collection includes front ends for C, C++, and Fortran as well as libraries for these languages
Go 1.11.5 1.11.5 Programming
Intel 17.0.1
18.0.2
18.0.2 Programming
LLVM 8.0.0 8.0.0 Programming The LLVM Compiler Collection includes the CLang front ends for C and C++ as well as libraries for these languages
Maple 2018.1 2018.1 Programming Maple is math software that combines the world's most powerful math engine with an interface that makes it extremely easy to analyze, explore, visualize, and solve mathematical problems.
  • Solve math problems easily and accurately, without worrying that you've lost a minus sign somewhere
  • Solve math problems quickly that you could never do by hand (or that you wouldn't want to do by hand because life is too short!)
  • Solve problems from virtually any branch of mathematics or field that relies on mathematics, such as calculus, algebra, differential equations, statistics, control design, linear algebra, physics, optimization, group theory, differential geometry, signal processing, special functions, number theory, financial modeling, etc. etc.
  • Gain insight into your problem, solution, data, or concept using a huge variety of customizable 2-D and 3-D plots and animations
  • Keep problems, solutions, visualizations, and explanations all together in a single, easy-to-follow document, so you don't have to waste time reconstructing your thought processes
  • Develop complex solutions using a sophisticated programming language designed for mathematics, so your code is shorter, easier to write, easier to debug, and easier to maintain
  • Create interactive applications for yourself, your students, or your colleagues, without having to be an expert programmer, and share them over the web
  • Mathematica 11.3.0 11.3.0 Programming Mathematica is a symbolic maths program.
    MATLAB R2015a
    R2016a
    R2017a
    R2018a
    R2018a Programming 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.
    R 3.3.1
    3.4.0
    3.4.0 Programming 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 AT&T, 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.
    ROOT 6.12.06 6.12.06 Programming ROOT is a modular scientific software framework. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage. It is mainly written in C++ but integrated with other languages such as Python and R.
    SWIG 3.0.12 3.0.12 Programming SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. SWIG is used with different types of target languages including common scripting languages such as Javascript, Perl, PHP, Python, Tcl and Ruby. The list of supported languages also includes non-scripting languages such as C#, Common Lisp (CLISP, Allegro CL, CFFI, UFFI), D, Go language, Java including Android, Lua, Modula-3, OCAML, Octave, Scilab and R. Also several interpreted and compiled Scheme implementations (Guile, MzScheme/Racket, Chicken) are supported. SWIG is most commonly used to create high-level interpreted or compiled programming environments, user interfaces, and as a tool for testing and prototyping C/C++ software. SWIG is typically used to parse C/C++ interfaces and generate the 'glue code' required for the above target languages to call into the C/C++ code. SWIG can also export its parse tree in the form of XML and Lisp s-expressions. SWIG is free software and the code that SWIG generates is compatible with both commercial and non-commercial projects.
    BEAGLE 2.1.2 2.1.2 Libraries 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.
    Bioconductor 3.5 3.5 Libraries Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1383 software packages, and an active user community.
    Biopython 1.67 1.67 Libraries 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 1.57.0-gcc
    1.61.0-gcc
    1.63.0-gcc
    1.63.0-intel
    1.70.0
    1.61.0-gcc Libraries 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)
    CGAL 4.9.1 4.9.1 Libraries CGAL is a software project that provides easy access to efficient and reliable geometric algorithms in the form of a C++ library. CGAL is used in various areas needing geometric computation, such as geographic information systems, computer aided design, molecular biology, medical imaging, computer graphics, and robotics. The library offers data structures and algorithms like triangulations, Voronoi diagrams, Boolean operations on polygons and polyhedra, point set processing, arrangements of curves, surface and volume mesh generation, geometry processing, alpha shapes, convex hull algorithms, shape analysis, AABB and KD trees...
    CheMPS2 1.8.9 1.8.9 Libraries CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry. This wavefunction method allows to obtain numerical accuracy in active spaces beyond the capabilities of full configuration interaction (FCI), and allows to extract the 2-, 3-, and 4-particle reduced density matrices (2-, 3- and 4-RDM) of the active space. For general active spaces up to 40 electrons in 40 orbitals can be handled with DMRG, and for one-dimensional active spaces up to 100 electrons in 100 orbitals. The 2-RDM of these active spaces can also be easily extracted, while the 3- and 4-RDM are limited to about 28 orbitals. When the active space size becomes prohibitively expensive for FCI, DMRG can be used to replace the FCI solver in the complete active space self consistent field (CASSCF) method and the corresponding complete active space second order perturbation theory (CASPT2). The corresponding methods are called DMRG-SCF and DMRG-CASPT2, respectively. For DMRG-SCF the active space 2-RDM is required, and for DMRG-CASPT2 the active space 4-RDM. CheMPS2 is designed for high-performance computers, with a hybrid parallelization for mixed distributed and shared memory architectures, realized with MPI and OpenMP. CheMPS2 is distributed under the GNU General Public License version 2, and can be downloaded from https://github.com/sebwouters/chemps2.
    CUDA 9.0
    9.1
    9.1 Libraries The NVIDIA® CUDA® Toolkit provides a development environment for creating high performance GPU-accelerated applications. With the CUDA Toolkit, you can develop, optimize and deploy your applications on GPU-accelerated embedded systems, desktop workstations, enterprise data centers, cloud-based platforms and HPC supercomputers. The toolkit includes GPU-accelerated libraries, debugging and optimization tools, a C/C++ compiler and a runtime library to deploy your application. GPU-accelerated CUDA libraries enable drop-in acceleration across multiple domains such as linear algebra, image and video processing, deep learning and graph analytics. For developing custom algorithms, you can use available integrations with commonly used languages and numerical packages as well as well-published development APIs. Your CUDA applications can be deployed across all NVIDIA GPU families available on premise and on GPU instances in the cloud. Using built-in capabilities for distributing computations across multi-GPU configurations, scientists and researchers can develop applications that scale from single GPU workstations to cloud installations with thousands of GPUs. The CUDA compiler (nvcc) defaults to g++ as it's C/C++ compiler. If you wish to use CUDA with the Intel compilers, you will need to set an envionment variable HOST_COMPILER to be equal to icpc. For example, using the default shell (BASH), you would do the following (either at the command line or in your .bashrc or .bash_profile login files): setenv HOST_COMPILER=icpc
    eigen 3.2.10
    3.3.1
    3.3.1 Libraries Eigen is a high-level C++ library of template headers for linear algebra, matrix and vector operations, geometrical transformations, numerical solvers and related algorithms.
    fftw 3.3.5 3.3.5 Libraries FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications.
    gflags 2.1.2 2.1.2 Libraries 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 0.3.5
    git-b6a5e05
    0.3.5 Libraries C++ implementation of the Google logging module.
    GSL 2.2.1
    2.4
    2.4 Libraries 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 1.10.0p1
    1.10.4
    1.10.5-parallel
    1.10.5-serial
    1.10.5-serial Libraries 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. This version is built for C, C++, and FORTRAN, but does not have any MPI support.
    HTSlib 1.3.2 1.3.2 Libraries This module provides the access to the Samtools HTSlib C Library. A C library for reading/writing high-throughput sequencing data.
    hwloc 2.0.3 2.0.3 Libraries The Hardware Locality (hwloc) software project aims at easing the process of discovering hardware resources in parallel architectures. It offers command-line tools and a C API for consulting these resources, their locality, attributes, and interconnection. hwloc primarily aims at helping high-performance computing (HPC) applications, but is also applicable to any project seeking to exploit code and/or data locality on modern computing platforms.
    isl 0.18 0.18 Libraries isl is a thread-safe C library for manipulating sets and relations of integer points bounded by affine constraints. The descriptions of the sets and relations may involve both parameters and existentially quantified variables. All computations are performed in exact integer arithmetic using GMP.
    KIM 1.7.3 1.7.3 Libraries 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.
    libffi 3.2.1 3.2.1 Libraries Compilers for high level languages generate code that follows certain conventions. These conventions are necessary, in part, for separate compilation to work. One such convention is the "calling convention". The "calling convention" is a set of assumptions made by the compiler about where function arguments will be found on entry to a function. A "calling convention" also specifies where the return value for a function is found. Some programs may not know at the time of compilation what arguments are to be passed to a function. For instance, an interpreter may be told at run-time about the number and types of arguments used to call a given function. Libffi can be used in such programs to provide a bridge from the interpreter program to compiled code. The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. FFI stands for Foreign Function Interface. A foreign function interface is the popular name for the interface that allows code written in one language to call code written in another language. The libffi library really only provides the lowest, machine dependent layer of a fully featured foreign function interface. A layer must exist above libffi that handles type conversions for values passed between the two languages.
    libgtextutils 0.7 0.7 Libraries libgtextutils Libraries compiles with GNU Compilers on the Kennesaw State HPC Cluster. Gordon Text Utilities
    OpenBLAS 0.2.19 0.2.19 Libraries OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. This environment module attempts to load the most appropriate version of OpenBLAS based on CPU capabilities.
    OpenMPI 1.6.4
    1.10.7
    2.1.1
    3.1.3
    4.0.1
    4.0.1 Libraries The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software vendors, application developers and computer science researchers.
    perl5-libs KSU-01 KSU-01 Libraries non-standard perl5-libs Libraries on the Kennesaw State HPC Cluster. These are perl5 libraries that other modules may depend on.
    Qt 4.8.7
    5.12.2
    5.12.2 Libraries
    ReportLab 3.3.12 3.3.12 Libraries 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.
    Szip 2.1.1 2.1.1 Libraries Szip compression software, providing lossless compression of scientific data, has been provided with HDF software products as of HDF5 Release 1.6.0 and HDF4 Release 2.0. Szip is an implementation of the extended-Rice lossless compression algorithm. The Consultative Committee on Space Data Systems (CCSDS) has adopted the extended-Rice algorithm for international standards for space applications. Szip is reported to provide fast and effective compression, specifically for the EOS data generated by the NASA Earth Observatory System (EOS). It was originally developed at University of New Mexico (UNM) and integrated with HDF4 by UNM researchers and developers. As the graphs to the right illustrate, the primary gain with Szip compression is in speed of processing. Szip also provides some advantage in compression ratio over other compression methods shown here. These results, including the data presented in the graphs below, are from tests conducted by Pen-Shu Yeh, et al., with the HDF4 Szip integration.
    TensorFlow-GPU 1.11.0 1.11.0 Libraries TensorFlow is an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more CPUs or GPUs in a desktop, server, or mobile device with a single API. TensorFlow was originally developed by researchers and engineers working on the Google Brain Team within Google's Machine Intelligence research organization for the purposes of conducting machine learning and deep neural networks research, but the system is general enough to be applicable in a wide variety of other domains as well.
    TensorFlow 1.2.0
    1.11.0
    1.11.0 Libraries TensorFlow is an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more CPUs or GPUs in a desktop, server, or mobile device with a single API. TensorFlow was originally developed by researchers and engineers working on the Google Brain Team within Google's Machine Intelligence research organization for the purposes of conducting machine learning and deep neural networks research, but the system is general enough to be applicable in a wide variety of other domains as well.
    Voro++ 0.4.6 0.4.6 Libraries 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 7.0.0
    8.1.0
    7.0.0 Libraries 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.
    z3 4.8.4 4.8.4 Libraries Z3 is a theorem prover from Microsoft Research. It is licensed under the MIT license. If you are not familiar with Z3, you can start https://github.com/Z3Prover/z3/wiki#background
    ABCluster 2.0 2.0 Software ABCluster/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap. Finishing capabilities include allowing the user to pick primers and templates, suggesting additional sequencing reactions to perform, and facilitating checking the accuracy of the assembly using digest and forward/reverse pair information.
    Abinit 8.0.8b 8.0.8b Software 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 2016Feb01 2016Feb01 Software 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).
    asciinema 1.4.0 1.4.0 Software Asciinema is a free and open source solution for recording the terminal sessions and sharing them on the web.
    AtomEye 2.2 2.2 Software AtomEye is an atomistic configuration viewer.
    AUGUSTUS 3.2.3 3.2.3 Software AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
    BamTools 2.4.1 2.4.1 Software BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
    BayeScan 2.1 2.1 Software BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model. One of the simplest possible scenarios covered consists of an island model in which subpopulation allele frequencies are correlated through a common migrant gene pool from which they differ in varying degrees. The difference in allele frequency between this common gene pool and each subpopulation is measured by a subpopulation specific FST coefficient. Therefore, this formulation can consider realistic ecological scenarios where the effective size and the immigration rate may differ among subpopulations.
    BCFtools 1.3.1 1.3.1 Software 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 2.4.20 2.4.20 Software 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 2.26.0 2.26.0 Software 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 1.1.2 1.1.2 Software 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 2.2.9 2.2.9 Software 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 2.0 2.0 Software 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 0.7.15 0.7.15 Software 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 1.3 1.3 Software Canu provides both a programmer's API and an end-user's toolkit for handling BAM files.
    Clustal-Omega 1.2.1 1.2.1 Software 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 2.1 2.1 Software Clustal W is a general purpose multiple alignment program for DNA or proteins.
    CompHEP 4.5.2 4.5.2 Software CompHEP: a package for evaluation of Feynman diagrams, integration over multi-particle phase space and event generation. This software requires that you create a working environment in your home directory to use. To create a working environment, use the following command: $ comphep-install.sh ${HOME}/comphep
    COMSOL 5.3a
    5.4
    5.4 Software COMSOL Multiphysics is a cross-platform finite element analysis, solver and multiphysics simulation software. It allows conventional physics-based user interfaces and coupled systems of partial differential equations.
    Consed 29.0 29.0 Software Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap. Finishing capabilities include allowing the user to pick primers and templates, suggesting additional sequencing reactions to perform, and facilitating checking the accuracy of the assembly using digest and forward/reverse pair information.
    Cufflinks 2.2.1 2.2.1 Software 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 3.3 3.3 Software DaliLite computes optimal and suboptimal structural alignments between two protein structures. It will compare all chains in the first structure against all chains in the second (unless specific chain IDs are given).
    Dialign 2.2.1 2.2.1 Software While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies.
    Doxygen 1.8.14 1.8.14 Software Doxygen is the de facto standard tool for generating documentation from annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba, Microsoft, and UNO/OpenOffice flavors), Fortran, VHDL, Tcl, and to some extent D.
    ELPH 1.0.1 1.0.1 Software ELPH is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences. The program takes as input a set containing anywhere from a few dozen to thousands of sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. We have used ELPH to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs). See below for instructions on downloading the complete system, including source code. An online tool that uses ELPH output for identifying exon splicing enhancers can be found here.
    EMBOSS 6.6.0 6.6.0 Software 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 20040222 20040222 Software 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 36.3.8c 36.3.8c Software The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
    FASTX-Toolkit 0.0.14 0.0.14 Software The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information). The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs. Example of such mapping programs are: Blat, SHRiMP, LastZ, MAQ and many many others. However, It is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome - manipulating the sequences to produce better mapping results. The FASTX-Toolkit tools perform some of these preprocessing tasks.
    FDist2 20020705 20020705 Software A program to detect loci that might be under selection in samples from structured populations.
    FFmpeg 2016Sept06 2016Sept06 Software 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 1.2.11 1.2.11 Software 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.
    FORM 4.2.0 4.2.0 Software FORM is a symbolic manipulation system. It reads text files containing definitions of mathematical expressions as well as statements that tell it how to manipulate these expressions. Its original author is Jos Vermaseren of Nikhef, the Dutch institute for subatomic physics. It is widely used in the theoretical particle physics community, but it is not restricted to applications in this specific field.
    FUSTr git-20190415 git-20190415 Software Fuster is a pipeline that clusters coding sequences from transcriptomes into protein families, and then analyzes those families for positive selection.
    GAMESS 18Aug2016 18Aug2016 Software GAMESS (US) can perform several general computational chemistry calculations, including Hartree–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 Møller–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 $END, which specifies that the SCF part of the code should do an restricted open-shell Hartree–Fock (ROHF) calculation and quit if the result does not converge in 30 iterations. The output is in an English language text file.
    Gblocks 0.91b 0.91b Software 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 4.5.1 4.5.1 Software 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 3.02b 3.02b Software 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 2016-05-01 2016-05-01 Software GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program
    gnuplot 5.0.3 5.0.3 Software 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 5.1.25 5.1.25 Software 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 2016.1
    2018
    2018-CUDA
    2016.1 Software 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 7.0.1
    7.5.2
    7.5.2 Software 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 6.19 6.19 Software 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 2.0.16
    3.0-beta.1
    3.0.0
    3.0.0 Software 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 3.1b2
    3.2.1
    3.2.1 Software 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.
    I-TASSER 4.4
    5.0
    5.0 Software 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.
    ImageMagick 7.0.3 7.0.3 Software 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 Béer curves.
    Jellyfish 2.2.6 2.2.6 Software 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 17Nov16
    30Jul16
    30Jul16-icc
    17Nov16 Software 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.
    lp_solve 5.5.2.5 5.5.2.5 Software lp_solve is a Mixed Integer Linear Programming (MILP) solver.
    luscus 0.8.1 0.8.1 Software 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. Kovačević, V. Veryazov, J. Cheminformatics, 7 (2015) 1-10; DOI: 10.1186/s13321-015-0060-z
    MAFFT 7.222
    7.273
    7.294
    7.294 Software 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. 
    MCNP 6.2 6.2 Software If you don't know what this package is for, you almost certanly don't have permission to use it. ************************************** ***** EXPORT CONTROLLED SOFTWARE ***** **************************************
    Modeller 9.16 9.16 Software 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 v8.0.15-06-18 v8.0.15-06-18 Software 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 5.7
    5.8
    5.8 Software 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.
    Molpro 2018.2.0 2018.2.0 Software Molpro is a comprehensive system of ab initio programs for advanced molecular electronic structure calculations, designed and maintained by H.-J. Werner and P. J. Knowles, and containing contributions from many other authors. It comprises efficient and well parallelized programs for standard computational chemistry applications, such as DFT with a large choice of functionals, as well as state-of-the art high-level coupled-cluster and multi-reference wave function methods. Electronically excited states can be treated using MCSCF/CASSCF, CASPT2, MRCI, or FCI methods, or by response methods such as TDDFT, CC2, and EOM-CCSD. There are many modules for computing molecular properties, geometry optimization, calculation of harmonic and anharmonic vibrational frequencies, and further wave function analysis. Analytical energy gradients are available for DFT, HF, MP2, MP2-F12, CCSD, CCSD-F12, DCSD, QCISD, QCISD(T), CASSCF, and CASPT2. Density fitting (DF or RI) approximations can speed up DFT and MP2 calculations with large basis sets by orders of magnitude, and explicitly correlated methods [MP2-F12, CCSD(T)-F12, CASPT2-F12, MRCI-F12] minimize basis set incompleteness errors to yield near CBS quality results with triple-zeta basis sets. Combined with local approximations and efficient parallelizations, high-level methods [PNO-LMP2-F12, PNO-LCCSD(T)-F12] can be be applied to large molecules of chemical interest, yielding unprecedented accuracy (for a recent review see WIREs Comput Mol Sci. 2018, e1371). Furthermore, WF-in-DFT embedding or QM/MM methods can be used to extend the applicability of ab initio methods to large systems of chemical or biochemical interest. A review with a number of benchmark examples can be found in H.-J. Werner, P. J. Knowles, G. Knizia, F. R. Manby and M. Schütz, WIREs Comput Mol Sci 2, 242-253 (2012), doi:10.1002/wcms.82. Molpro is very easy to use for standard applications, but also includes many advanced options for expert applications. It runs under UNIX/Linux (2.6.32 kernel onwards) and OS-X (Mountain Lion onwards). Molpro can also be used as a platform for development. The Molpro team constantly works on improving and extending the functionality and documentation of the program. Any suggestions for improvements are welcome and should be sent to molpro@molpro.net.
    mothur 1.37.4 1.37.4 Software 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 3.2.6
    3.2.6-intel
    3.2.6 Software MrBayes 3 is a program for Bayesian inference and model choice across a large space of phylogenetic and evolutionary models.
    MT-Toolbox 4.1.2 4.1.2 Software 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
    MToolBox 0.3.3 0.3.3 Software 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.
    MUSCLE 3.8.31
    3.8.1551
    3.8.1551 Software 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.
    NBO 7.0 7.0 Software The NBO program performs the analysis of a many-electron molecular wavefunction in terms of localized electron-pair bonding units. The program carries out the determination of natural atomic orbitals (NAOs), natural hybrid orbitals (NHOs), natural bond orbitals (NBOs), and natural localized molecular orbitals (NLMOs), and uses these to perform natural population analysis (NPA), NBO energetic (deletions) analysis, and other tasks pertaining to localized analysis of wavefunction properties, including natural resonance theory (NRT) and natural chemical shielding (NCS) analysis. This section provides a brief introduction to NBO algorithms and nomenclature.
    NCBI-Blast 2.3.0+ 2.3.0+ Software 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.
    Netpbm 10.73.17 10.73.17 Software The netpbm package contains a library of functions which support programs for handling various graphics file formats, including .pbm (portable bitmaps), .pgm (portable graymaps), .pnm (portable anymaps), .ppm (portable pixmaps) and others.
    OpenBabel 2.4.1 2.4.1 Software Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Installed are the GUI, Command Line Tools, and language bindings for Python, Perl, and Java.
    OpenFOAM 4.1 4.1 Software OpenFOAM is the leading free, open source software for computational fluid dynamics (CFD), owned by the OpenFOAM Foundation and distributed exclusively under the General Public Licence (GPL). The GPL gives users the freedom to modify and redistribute the software and a guarantee of continued free use, within the terms of the licence.
    PAML 4.9i 4.9i Software PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained by Ziheng Yang and distributed under the GNU GPL v3. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.
    ParaView 5.2.0 5.2.0 Software 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.
    phd2fasta 130911 130911 Software Phred and consed write sequence and quality value information in 'phd' output files. A phd file contains information in a header, the called bases, the base quality values, and the base call trace locations. Phd2fasta reads phd files and writes sequence and quality value FASTA files, which phrap and cross_match need as input. (Consed needs phd files in order to obtain the base call locations.)
    Phrap 1.090518 1.090518 Software The phrap module contains three pieces of related software: phrap, cross_match, and swat. phrap is a program for assembling shotgun DNA sequence data. Among other features, it allows use of the entire read and not just the trimmed high quality part, it uses a combination of user-supplied and internally computed data quality information to improve assembly accuracy in the presence of repeats, it constructs the contig sequence as a mosaic of the highest quality read segments rather than a consensus, it provides extensive assembly information to assist in trouble-shooting assembly problems, and it handles large datasets. cross_match is a general purpose utility for comparing any two DNA sequence sets using a 'banded' version of swat. For example, it can be used to compare a set of reads to a set of vector sequences and produce vector-masked versions of the reads, a set of cDNA sequences to a set of cosmids, contig sequences found by two alternative assembly procedures (for example, phrap and xbap) to each other, or phrap contigs to the final edited cosmid sequence. It is slower but more sensitive than BLAST. swat is a program for searching one or more DNA or protein query sequences, or a query profile, against a sequence database, using an efficient implementation of the Smith-Waterman or Needleman-Wunsch algorithms with linear (affine) gap penalties. For each match an empirical measure of statistical significance derived from the observed score distribution is computed.
    Phred 020425
    071220
    020425 Software Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files. Phred can read trace data from chromatogram files in the SCF, ABI, and ESD formats. It automatically determines the file format, and whether the chromatogram file was compressed using gzip, bzip2, or UNIX compress. After calling bases, phred writes the sequences to files in either FASTA format, the format suitable for XBAP, PHD format, or the SCF format. Quality values for the bases are written to FASTA format files or PHD files, which can be used by the phrap sequence assembly program in order to increase the accuracy of the assembled sequence.
    PHYLIP 3.696 3.696 Software 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.
    PhyML 3.1 3.1 Software 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 2.3.7 2.3.7 Software 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 1.12 1.12 Software 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 3D 3D Software 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 3.4.2 3.4.2 Software 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 1.8.2.1 1.8.2.1 Software PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating 3D molecular structures.
    qhost 1.3.1
    1.3.1.1
    1.3.1.1 Software 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 0.7.2 0.7.2 Software 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 0.1.19
    1.3.1
    1.3.1 Software 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.
    SCOTCH 6.0.6-gcc
    6.0.6-icc
    6.0.6-gcc Software SCOTCH is a project carried out within the Satanas team of the Laboratoire Bordelais de Recherche en Informatique (LaBRI). It is part of the ScAlApplix project of INRIA Bordeaux - Sud-Ouest. Its purpose is to apply graph theory, with a divide and conquer approach, to scientific computing problems such as graph and mesh partitioning, static mapping, and sparse matrix ordering, in application domains ranging from structural mechanics to operating systems or bio-chemistry. The SCOTCH distribution is a set of programs and libraries which implement the static mapping and sparse matrix reordering algorithms developed within the SCOTCH project.
    SeaView 4.6.1 4.6.1 Software 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.
    SediFoam 20180922 20180922 Software SediFoam is a hybrid CFD-DEM solver for particle-laden flows based on two open-source codes: OpenFOAM, an object-oriented CFD platform by OpenCFD, and LAMMPS, a highly efficient molecular dynamics solver by Sandia National Laboratories. SediFoam Version: 20180922 OpenFOAM Version: 2.4.0 LAMMPS Version: 1Feb14
    SiLiX 1.2.11 1.2.11 Software The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints.
    Simcoal2 2.1.2 2.1.2 Software A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models.
    SQLite 3.27.2 3.27.2 Software SQLite is a C-language library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine. SQLite is the most used database engine in the world. SQLite is built into all mobile phones and most computers and comes bundled inside countless other applications that people use every day.
    TeXLive 2016 2016 Software 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.
    Tinker 8.4.3 8.4.3 Software The Tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. Tinker has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22/CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable model, and the AMOEBA (2004, 2009, 2013) polarizable atomic multipole force field. Parameter sets for other widely-used force fields are under consideration for future releases.
    TopHat 2.1.1 2.1.1 Software 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 2.1.1
    2.2.0
    2.2.0 Software 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 490848f 490848f Software 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 1.2.10
    1.2.10-maxk63-big
    1.2.10-maxk63-categ14-big
    1.2.10 Software Velvet is a sequence assembler for very short reads.
    Vim 8.1.20180822 8.1.20180822 Software VIM (VIsual editor iMproved) is an updated and improved version of the vi editor. Vi was the first real screen-based editor for UNIX, and is still very popular. VIM improves on vi by adding new features: multiple windows, multi-level undo, block highlighting and more.
    VMD 1.9.2
    1.9.3-gpu
    1.9.3-text
    1.9.2 Software 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 2.4.1 2.4.1 Software 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.

    Data last updated at: Tue Apr 30 15:58:35 EDT 2019

    • available_software.txt
    • Last modified: 2019/04/30 20:02
    • by eeidson