HPC Software List – University of Alabama Research Computing

Software Categories:

Our software offerings comprise diverse applications that serve distinct domains, furnishing robust instruments for scholarly investigation, scientific inquiry, and vocational tasks. Whether one assumes the role of a scholar, investigator, or practitioner, our software solutions present inventive methodologies and cutting-edge functionalities to facilitate their pursuits.

Software Catalog:

Software Name	Category	Description	Documentation
Matlab	Mathematics	Numeric computing and programming environment for engineers/scientists.	View
Mathematica	Mathematics	Symbolic and numerical computations, data analysis, visualization.	View
Gurobi	Mathematics	Powerful mathematical optimization solver for large-scale problems.	View
Cplex	Mathematics	CPLEX is a high-performance mathematical optimization solver.	View
R	Mathematics	Open-source language for statistical computing and graphics.	View
Adcirc	Mathematics	ADCIRC is a numerical model for storm surge forecasting.	View
FFTW	Mathematics	FFTW is a fast Fourier transform library	View
Num Utils	Mathematics	Numutils is a collection of numerical libraries.	View
Octave	Mathematics	Octave is a high-level language for numerical computations.	View
Petsc	Mathematics	PETSc is a library for scalable scientific computing.	View
Comsol	Physics	COMSOL is a multiphysics simulation software platform.	View
Grass	GIS	GRASS GIS is a free geospatial analysis software.	View
LLAMPS	Physics	LLAMPS is a molecular dynamics simulation software package.	View
QEspresso	Physics	Quantum ESPRESSO is a package for materials modeling.	View
Sprnt	GIS	SPRNT is a river dynamics simulation software package.	View
GDAL	GIS	GDAL is a library for geospatial data processing.	View
GeOS	GIS	GEOS is a C++ library for geometric operations.	View
Gromacs	Physics	GROMACS is a molecular dynamics simulation software package.	View
Lhapdf	Physics	LHAPDF is a library for high-energy physics.	View
Metis	Physics	METIS is a graph partitioning and meshing tool.	View
Moose	Physics	MOOSE is a framework for multiphysics simulation.	View
NCL NCAR	GIS	NCL is a data analysis and visualization tool for atmospheric and oceanic sciences.	View
Nx Nastran	Physics	NX Nastran is a finite element analysis software.	View
OpenAL	Physics	OpenAL is an open-source 3D audio library.	View
Parmetis	Physics	ParMETIS is a parallel graph partitioning library.	View
Phana	Physics	Phana is a software package for analyzing phonon properties.	View
Phreeqcrm	Chemistry	Phreeqcrm is a geochemical modeling software package.	View
Proj	GIS	PROJ is a cartographic projection software library.	View
Pythia	Physics	Pythia is a particle physics event generator software.	View
Questa	Physics	Questa is a digital verification and simulation software.	View
SFML	Physics	SFML is a multimedia library for game development.	View
Gaussian	Chemistry	Gaussian is a quantum chemistry software package.	View
Orca	Chemistry	Orca is a quantum chemistry software package.	View
Q-chem	Chemistry	Q-Chem is a quantum chemistry simulation software.	View
Allpaths	Biology	Genome assembly software for large and complex genomes.	View
Augustus	Biology	Ab initio gene prediction software for eukaryotic genomes.	View
BBmap	Biology	Fast and accurate nucleotide sequence alignment software.	View
Blast	Biology	Sequence similarity search software for nucleotide/protein databases.	View
Bamtools	Biology	Fast and accurate nucleotide sequence alignment software.	View
Bismark	Biology	Bisulfite sequence alignment and methylation analysis software.	View
Bowtie	Biology	Ultrafast and memory-efficient nucleotide sequence alignment software.	View
Blat	Biology	Rapid sequence alignment software for nucleotide sequences.	View
Braker	Biology	Gene prediction software for RNA-seq data.	View
Busco	Biology	Evaluation of genome assembly and annotation completeness software.	View
Cufflinks	Biology	Transcriptome assembly and differential expression analysis software.	View
Edta	Biology	Retrotransposon identification and removal software for genome assembly.	View
Fastimcoal	Biology	Fast and efficient coalescent simulation software for population genetics.	View
Fastqc	Biology	Quality control tool for high-throughput sequencing data.	View
Faststructures	Biology	Software for Bayesian analysis of population structure.	View
Freesurfer	Biology	Software suite for brain MRI image analysis.	View
Fsl	Biology	Software library for neuroimaging data analysis.	View
Hisat	Biology	Hierarchical indexing for spliced alignment of transcripts.	View
InterProScan	Biology	Protein functional analysis software using multiple databases.	View
LTR retriever	Biology	Software for identifying and annotating LTR retrotransposons.	View
Last	Biology	Software for finding similar regions between sequences.	View
Maker	Biology	Genome annotation software for eukaryotic organisms.	View
Masurca	Biology	Hybrid genome assembly software for large and complex genomes.	View
Miniasm	Biology	Ultrafast de novo assembly software for long reads.	View
Minimap	Biology	Software for mapping long noisy sequencing reads.	View
Mira	Biology	De novo genome assembly software for next-generation sequencing data.	View
Nanopolish	Biology	Software for signal-level analysis of nanopore sequencing data.	View
Organell	Biology	Software for assembling and annotating organellar genomes.	View
Orthofinder	Biology	Software for identifying orthologous genes among multiple species.	View
Porechop	Biology	Software for adapter trimming of nanopore sequencing data.	View
Qiime	Biology	Software for analyzing microbial communities from DNA sequencing data.	View
Quast	Biology	Quality assessment tool for genome assemblies.	View
Raxml	Biology	Software for maximum likelihood phylogenetic tree inference.	View
Repeat Modeler	Biology	Software for de novo repeat family identification and modeling.	View
Salmon	Biology	Software for fast and accurate transcript quantification from RNA-seq.	View
Samtools	Biology	Software for manipulating and analyzing SAM/BAM format files.	View
Stacks	Biology	Software for population genomics analysis using restriction site-associated DNA.	View
Supernova	Biology	Software for de novo genome assembly from linked-read sequencing data.	View
Transdecoder	Biology	Software for identifying candidate coding regions within transcript sequences.	View
Transposome	Biology	Software for identification and annotation of transposable elements.	View
Trinity	Biology	De novo transcriptome assembly software from RNA-seq data.	View
Bam-readcount	Biology	Software for counting aligned reads at genomic positions.	View
Bgc	Biology	Software for identifying and analyzing biosynthetic gene clusters.	View
Diyabc	Biology	Software for inferring demographic history using molecular markers.	View
Evidence Modeler(EVM)	Biology	Software for integrating evidence for genome annotation.	View
Genemark	Biology	SAb initio gene prediction software for prokaryotic and eukaryotic genomes.	View
Generax	Biology	Software for genome and transcriptome assembly and annotation.	View
Gmap	Biology	Software for mapping and aligning cDNA and genomic sequences.	View
Grid	Biology	Software for analyzing genetic data from pedigrees.	View
Hifiasm	Biology	De novo assembly software for highly heterozygous diploid genomes.	View
Hmmer	Biology	Software for protein sequence analysis using hidden Markov models.	View
HyPhy	Biology	Software for analyzing genetic sequence data for molecular evolution.	View
Ima2p	Biology	Software for protein sequence analysis using hidden Markov models.	View
Ima2p	Biology	Software for inferring demographic history using SNP data.	View
Ivc(Issac)	Biology	Software for correcting sequencing errors in Illumina reads using k-mer frequencies.	View
Jags	Biology	Software for Bayesian statistical analysis using Markov Chain Monte Carlo simulation.	View
Kallisto	Biology	Software for quantifying transcript abundances from RNA-seq data.	View
Kraken	Biology	Software for taxonomic classification of metagenomic sequencing data using k-mers.	View
Meraculous	Biology	De novo genome assembly software for large and complex genomes using Illumina reads.	View
Modeltest NG	Biology	Software for selecting the best-fitting model of nucleotide or amino acid substitution for phylogenetic analysis.	View
Mricron	Biology	MRI image viewer and analysis software tool.	View
Nanosim	Biology	Nanosim is a simulation tool for nanopore sequencing.	View
NextDenovo	Biology	NextDenovo is a string graph-based de novo assembler for long reads	View
Nextpolish	Biology	NextPolish is a software for polishing long-read assemblies.	View
Pbsuite	Biology	PBsuite is a suite of bioinformatics tools for PacBio long-read sequencing data analysis.	View
Phylobayes	Biology	Bayesian inference of phylogenies from DNA/RNA data.	View
Poretally	Biology	Benchmark nanopore assembly pipelines using poreTally.	View
Price	Biology	Price is a de novo genome assembler.	View
pyRad	Biology	pyRAD: Python-based restriction site associated DNA analysis.	View
Racer	Biology	Hybrid assembly correction tool for long reads.	View
Racon	Biology	Racon is a consensus module for long-read assemblers.	View
Redundans	Biology	Redundans: reduce redundancy and improve genome assembly.	View
Sga	Biology	SGA: de Bruijn graph-based genome assembly tool.	View
SPAdes	Biology	SPAdes: de novo assembly of microbial genomes.	View
Sra toolkit	Biology	NCBI SRA file format conversion and manipulation tool.	View
Star	Biology	Star is a fast RNA-seq aligner.	View
Velvet	Biology	Velvet is a de novo short read assembler.	View
Boost	Utilities	Portable source-level C++ libraries and development tools.	View
Charm ++	Utilities	Parallel programming system with dynamic load balancing.	View
HPC Compilers	Utilities	Collection of installed compilers on HPC	View
Cuda	Utilities	Parallel computing platform and programming model developed by NVIDIA	View
Eigen	Utilities	C++ template library for linear algebra	View
Go	Utilities	Open source programming language for networked computing.	View
Gsl	Utilities	C library for numerical computations and statistics.	View
Julia	Utilities	High-level dynamic programming language for technical computing.	View
NetCDF	Utilities	Data format and software for scientific data access.	View
Perl	Utilities	High-level scripting language for text manipulation.	View
Pgi	Utilities	High-performance optimizing compilers for parallel computing.	View
Ruby	Utilities	Dynamic, open source programming language with elegance.	View
Singularity	Utilities	Containerization platform for scientific and high-performance computing.	View
Spark	Utilities	Distributed computing system for big data processing.	View
Valgrind	Utilities	Dynamic analysis tools for debugging and profiling.	View
Conda	Utilities	Package manager for Python (and more).	View
TCL/TK	Utilities	TCL/TK: GUI development with easy scripting language.	View
Trimgalore	Biology	Adapter trimming tool for next-gen sequencing data.	View
WRF-Hydro	GIS	Hydrological modeling system for simulating water cycle.	View
Udunits	Utilities	Library for handling units of physical quantities.	View
VCF Tools	Biology	Utility for manipulating variant call format files.	View