| Software Item | Details | ||||||
|---|---|---|---|---|---|---|---|
| espresso | Quantum ESPRESSO is an integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale.
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| evidence-modeler | EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures.
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| evolver | Surface Evolver is an interactive program for the modelling of liquid surfaces shaped by various forces and constraints
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| exabayes | ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters.
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| examl | Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI. This code implements the popular RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.
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| exonerate | Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.
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| express | eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.
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| extrae | Instrumentation framework to generate execution traces of the most used parallel runtimes.
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| fastgear | Software for analysing sequence alignments
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| fastme | A comprehensive, accurate and fast distance-based phylogeny inference program
|
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| fastml | Used for the reconstruction of ancestral sequences. gub version adds functionality for gubbins software
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| fastool | Simple and quick FastQ and FastA tool for file reading and conversion
|
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| fastqc | A quality control tool for high throughput sequence data.
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| fastStructure | fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.
|
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| fasttree | FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.
|
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| fastx-toolkit | The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
|
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| fdmnes | FDMNES is an ab initio, free and open source, parallelled under MPI, code which calculates the XANES, RXS and XMCD spectra.
|
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| fds | Fire Dynamics Simulator (FDS) is a computational fluid dynamics (CFD) model of fire-driven fluid flow. The software solves numerically a form of the Navier-Stokes equations appropriate for low-speed, thermally-driven flow, with an emphasis on smoke and heat transport from fires.
|
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| fdtd-solutions | [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] Lumerical FDTD Solutions is a high performance 3D FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials.
|
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| ferret | This software is Open Source. Ferret is an interactive computer visualization and analysis environment.
|
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| ffmpeg | FFMPEG is a complete, cross-platform solution to record, convert and stream audio and video.
|
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| fftw | Libraries for computation of discrete Fourier transform.
|
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| fiji | Fiji is an image processing package—(a batteries-included) distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
|
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| flappie | flappie: Basecall Fast5 reads using flip-flop basecalling
|
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| flex | Lexical analyser generators
|
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| flexbar | The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences.
|
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| flexlm | FLEXlm utility programs.
|
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| flux-utils | flux-utils is a collection of utilities for the Flux and Armis HPC clusters.
|
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| freebayes | Bayesian genetic variant detector designed to find small polymorphisms
|
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| freesurfer | FreeSurfer MRI processing and analysis software.
|
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| fsl | FSL suite of MRI neuroimaging tools.
|
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| g95 | G95 – f95/f90 fortran compiler
|
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| GAMESS | The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.
|
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| gatk | The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it’s a suite of tools for working with the human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and local realigner.
|
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| gaussian | Gaussian is an electronic structure program that predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types.
|
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| gcc | GNU compiler suite
|
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| gdal | GDAL is a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation.
|
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| gdal-h4 | GDAL is a translator library for raster and vector geospatial data formats
|
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| geant | is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
|
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| gemini | GEMINI – integrative exploration of genetic variation and genome annotations.
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Total pages: 13
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