| Software Item | Details | ||||||
|---|---|---|---|---|---|---|---|
| abaqus | Abaqus FEA product suite for engineering problems: vehicle loads, dynamic vibration, multibody systems, impact/crash, nonlinear static, thermal coupling, and acoustic-structural coupling.
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| abinit | 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 basis.
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| absoft_profortran | [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] Absoft Pro Fortran Compiler
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| adapterremoval | This program searches for and removes remnant adapter sequences from your read data. The program can analyze both single end and paired end data. For detailed explanation of the parameters, please refer to the man page. For comments, suggestions and feedback please contact Stinus Lindgreen (stinus@binf.ku.dk) and Mikkel Schubert (MikkelSch@gmail.com).
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| admixture | software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.
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| adtex | Aberration Detection in Tumour Exome
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| aenet | Atomic Energy Network (aenet) is a software package [1] for the construction and usage of atomic interaction potentials based on artificial neural networks.
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| afni | AFNI suite of MRI neuroimaging tools.
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| allele-seq | Allele Specific Expression and Binding in a Network Framework
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| allinea_forge | Parallel debugging and profiling tools, DDT and MAP.
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| allinea_reports | Parallel profiling tool.
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| almabte | This software is Open Source. almaBTE consists of a library and a collection of executables allowing the user to calculate thermal transport properties of heterogeneous structures, using only ab-initio data, and solving the phonon Boltzmann Transport Equation (BTE).
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| amber | Amber refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.
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| ampl | AMPL algebraic modelling language.
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| annovar | ANNOVAR is a software tool to functionally annotate genetic variants detected from diverse genomes
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| ansys | ANSYS is a finite element simulation tool for multiphysics simulations.
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| ansysem | ANSYS EM: HFSS and Maxwell
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| antismash | a swiss-army knife of tools for a wide-range of genomics analysis tasks.
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| antlr | ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, processing, executing, or translating structured text or binary files.
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| ANTs | ANTs MRI image registration program
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| ANTsR | R with ANTsR available via site libraries.
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| anvio | Anvi’o is an analysis and visualization platform for ‘omics data.
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| arc-admin-utils | ARC Admin Utilities
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| ariba | A tool that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling..
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| armadillo | A high quality linear algebra library (matrix maths) for C++ language, aiming towards a good balance between speed and ease of use
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| ase | Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
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| ASTRID | ASTRID: Accurate Species TRees from Internode Distances. ASTRID is a ILS-aware tool for species tree estimation.
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| ataqv | A toolkit for measuring and comparing ATAC-seq results
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| atomicrex | Atomicrex is a general purpose tool for the construction of atomic interaction models
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| augustus | AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
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| bam-readcount | The purpose of bam-readcount is to generate metrics at single nucleotide positions. There are number of metrics generated which can be useful for filtering out false positive calls.
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| bamql | BAMQL filters SAM or BAM files using a simple query language that is more expressive than the view options available in samtools.
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| bamtools | BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files.
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| bamUtil | Perform operations on SAM/BAM files
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| bayescan | 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 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.
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| BayesTraits | BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available.
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| bbmap | BBMap, a short read aligner, as well as various other bioinformatic tools
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| bcftools | BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF
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| beagle | BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.
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| beast | BEAST is a software package for phylogenetic analysis with an emphasis on time-scaled trees.
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Total pages: 13
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