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 Categories
- Physics: Our physics software solutions provide advanced simulations and analyses of physical phenomena, covering classical mechanics, electromagnetism, and quantum mechanics. These tools offer powerful modeling and visualization capabilities for exploring and understanding the fundamental laws of the universe.
- Mathematics: Our mathematics software solutions provide comprehensive coverage of mathematical concepts, from data analysis to advanced modeling and scientific computation. These tools offer a variety of approaches and techniques for solving mathematical problems and analyzing complex systems.
- Chemistry: Our software solutions for quantum chemistry equip researchers with advanced instruments to scrutinize and interpret chemical properties, encompassing molecular structures and reaction kinetics. These instruments provide potent visualization and analysis capabilities to unravel chemical mechanisms and devise novel materials.
- Biology: Our biology software solutions provide cutting-edge tools for analyzing complex biological systems and processes, covering topics such as genomics, proteomics, and biomedical engineering. These tools offer powerful data visualization and analysis capabilities for understanding the underlying mechanisms of life.
- GIS: Our GIS software solutions provide sophisticated tools for spatial analysis, mapping, and visualization. These tools offer powerful capabilities for exploring geographic data, creating custom maps, and analyzing complex spatial relationships across various domains, including urban planning, environmental management, and transportation engineering.
- Utilities: Our utilities software solutions provide tools like compilers and container software to streamline HPC workflow, improve performance, and boost productivity.
Software Downloads
Visit the OIT Software Catalog to see available software downloads.
- XQuartz – Download the version under “Quick Download”
- MobaXterm – Download MobaXterm package
- Putty – Download the Windows MSI Installer Package
- Xming – Download xming-6-9-0-31-setup.exe
- WinSCP – Download the Installation package
Software Support Services
We offer the following services for software installation:
- Maintain user accounts linked with myBama usernames and automatic VPN access
- Documentation & training
- Multiple storage options
- Globus endpoints for high-speed data transfer
- Hardware monitoring with repair oversight
- Cluster scheduler monitoring
- Security monitoring
Software List
| Software Title | Category | Description | Documentation |
|---|---|---|---|
| Matlab | Mathematics | Numeric computing and programming environment for engineers/scientists. | View Matlab |
| Mathematica | Mathematics | Symbolic and numerical computations, data analysis, visualization. | View Mathematica |
| Gurobi | Mathematics | Powerful mathematical optimization solver for large-scale problems. | View Gurobi |
| Cplex | Mathematics | CPLEX is a high-performance mathematical optimization solver. | View Cplex |
| R | Mathematics | Open-source language for statistical computing and graphics. | View R |
| Adcirc | Mathematics | ADCIRC is a numerical model for storm surge forecasting. | View Adcirc |
| Num Utils | Mathematics | Numutils is a collection of numerical libraries. | View Num Utils |
| Octave | Mathematics | Octave is a high-level language for numerical computations. | View Octave |
| Petsc | Mathematics | PETSc is a library for scalable scientific computing. | View Petsc |
| Comsol | Physics | COMSOL is a multiphysics simulation software platform. | View Comsol |
| Grass | GIS | GRASS GIS is a free geospatial analysis software. | View Grass |
| LLAMPS | Physics | LLAMPS is a molecular dynamics simulation software package. | View LLAMPS |
| QEspresso | Physics | Quantum ESPRESSO is a package for materials modeling. | View QEspresso |
| Sprnt | GIS | SPRNT is a river dynamics simulation software package. | View Sprnt |
| GDAL | GIS | GDAL is a library for geospatial data processing. | View GDAL |
| GeOS | GIS | GEOS is a C++ library for geometric operations. | View GeOS |
| Gromacs | Physics | GROMACS is a molecular dynamics simulation software package. | View Gromacs |
| Lhapdf | Physics | LHAPDF is a library for high-energy physics. | View Lhapdf |
| Metis | Physics | METIS is a graph partitioning and meshing tool. | View Metis |
| Moose | Physics | MOOSE is a framework for multiphysics simulation. | View Moose |
| NCL NCAR | GIS | NCL is a data analysis and visualization tool for atmospheric and oceanic sciences. | View NCL NCAR |
| Nx Nastran | Physics | NX Nastran is a finite element analysis software. | View Nx Nastran |
| OpenAL | Physics | OpenAL is an open-source 3D audio library. | View OpenAL |
| Parmetis | Physics | ParMETIS is a parallel graph partitioning library. | View Parmetis |
| Phana | Physics | Phana is a software package for analyzing phonon properties. | View Phana |
| Phreeqcrm | Chemistry | Phreeqcrm is a geochemical modeling software package. | View Phreeqcrm |
| Proj | GIS | PROJ is a cartographic projection software library. | View Proj |
| Pythia | Physics | Pythia is a particle physics event generator software. | View Pythia |
| Questa | Physics | Questa is a digital verification and simulation software. | View Questa |
| SFML | Physics | SFML is a multimedia library for game development. | View SFML |
| Gaussian | Chemistry | Gaussian is a quantum chemistry software package. | View Gaussian |
| Orca | Chemistry | Orca is a quantum chemistry software package. | View Orca |
| Q-chem | Chemistry | Q-Chem is a quantum chemistry simulation software. | View Q-chem |
| Allpaths | Biology | Genome assembly software for large and complex genomes. | View Allpaths |
| Augustus | Biology | Ab initio gene prediction software for eukaryotic genomes. | View Augustus |
| BBmap | Biology | Fast and accurate nucleotide sequence alignment software. | View BBmap |
| Blast | Biology | Sequence similarity search software for nucleotide/protein databases. | View Blast |
| Bamtools | Biology | Fast and accurate nucleotide sequence alignment software. | View Bamtools |
| Bismark | Biology | Bisulfite sequence alignment and methylation analysis software. | View Bismark |
| Bowtie | Biology | Ultrafast and memory-efficient nucleotide sequence alignment software. | View Bowtie |
| Blat | Biology | Rapid sequence alignment software for nucleotide sequences. | View Blat |
| Braker | Biology | Gene prediction software for RNA-seq data. | View Braker |
| Busco | Biology | Evaluation of genome assembly and annotation completeness software. | View Busco |
| Cufflinks | Biology | Transcriptome assembly and differential expression analysis software. | View Cufflinks |
| Edta | Biology | Retrotransposon identification and removal software for genome assembly. | View Edta |
| Fastimcoal | Biology | Fast and efficient coalescent simulation software for population genetics. | View Fastimcoal |
| Fastqc | Biology | Quality control tool for high-throughput sequencing data. | View Fastqc |
| Faststructures | Biology | Software for Bayesian analysis of population structure. | View Faststructures |
| Freesurfer | Biology | Software suite for brain MRI image analysis. | View Freesurfer |
| Fsl | Biology | Software library for neuroimaging data analysis. | View Fsl |
| Hisat | Biology | Hierarchical indexing for spliced alignment of transcripts. | View Hisat |
| InterProScan | Biology | Protein functional analysis software using multiple databases. | View InterProScan |
| LTR retriever | Biology | Software for identifying and annotating LTR retrotransposons. | View LTR Retriever |
| Last | Biology | Software for finding similar regions between sequences. | View Last |
| Maker | Biology | Genome annotation software for eukaryotic organisms. | View Maker |
| Masurca | Biology | Hybrid genome assembly software for large and complex genomes. | View Masurca |
| Miniasm | Biology | Ultrafast de novo assembly software for long reads. | View Miniasm |
| Minimap | Biology | Software for mapping long noisy sequencing reads. | View Minimap |
| Mira | Biology | De novo genome assembly software for next-generation sequencing data. | View Mira |
| Nanopolish | Biology | Software for signal-level analysis of nanopore sequencing data. | View Nanopolish |
| Organell | Biology | Software for assembling and annotating organellar genomes. | View Organell |
| Orthofinder | Biology | Software for identifying orthologous genes among multiple species. | View Orthofinder |
| Porechop | Biology | Software for adapter trimming of nanopore sequencing data. | View Porechop |
| Qiime | Biology | Software for analyzing microbial communities from DNA sequencing data. | View Qiime |
| Quast | Biology | Quality assessment tool for genome assemblies. | View Quast |
| Raxml | Biology | Software for maximum likelihood phylogenetic tree inference. | View Raxml |
| Repeat Modeler | Biology | Software for de novo repeat family identification and modeling. | View Repeat Modeler |
| Salmon | Biology | Software for fast and accurate transcript quantification from RNA-seq. | View Salmon |
| Samtools | Biology | Software for manipulating and analyzing SAM/BAM format files. | View Samtools |
| Stacks | Biology | Software for population genomics analysis using restriction site-associated DNA. | View Stacks |
| Supernova | Biology | Software for de novo genome assembly from linked-read sequencing data. | View Supernova |
| Transdecoder | Biology | Software for identifying candidate coding regions within transcript sequences. | View Transdecoder |
| Transposome | Biology | Software for identification and annotation of transposable elements. | View Transposome |
| Trinity | Biology | De novo transcriptome assembly software from RNA-seq data. | View Trinity |
| Bam-readcount | Biology | Software for counting aligned reads at genomic positions. | View Bam-readcount |
| Bgc | Biology | Software for identifying and analyzing biosynthetic gene clusters. | View Bgc |
| Diyabc | Biology | Software for inferring demographic history using molecular markers. | View Diyabc |
| Evidence Modeler(EVM) | Biology | Software for integrating evidence for genome annotation. | View Evidence Modeler(EVM) |
| Genemark | Biology | SAb initio gene prediction software for prokaryotic and eukaryotic genomes. | View Genemark |
| Generax | Biology | Software for genome and transcriptome assembly and annotation. | View Generax |
| Gmap | Biology | Software for mapping and aligning cDNA and genomic sequences. | View Gmap |
| Grid | Biology | Software for analyzing genetic data from pedigrees. | View Grid |
| Hifiasm | Biology | De novo assembly software for highly heterozygous diploid genomes. | View Hifiasm |
| Hmmer | Biology | Software for protein sequence analysis using hidden Markov models. | View Hmmer |
| HyPhy | Biology | Software for analyzing genetic sequence data for molecular evolution. | View HyPhy |
| Ima2p | Biology | Software for protein sequence analysis using hidden Markov models. | View Ima2p |
| Ima2p | Biology | Software for inferring demographic history using SNP data. | View Ima2p |
| Ivc(Issac) | Biology | Software for correcting sequencing errors in Illumina reads using k-mer frequencies. | View Ivc(Issac) |
| Jags | Biology | Software for Bayesian statistical analysis using Markov Chain Monte Carlo simulation. | View Jags |
| Kallisto | Biology | Software for quantifying transcript abundances from RNA-seq data. | View Kallisto |
| Kraken | Biology | Software for taxonomic classification of metagenomic sequencing data using k-mers. | View Kraken |
| Meraculous | Biology | De novo genome assembly software for large and complex genomes using Illumina reads. | View Meraculous |
| Modeltest NG | Biology | Software for selecting the best-fitting model of nucleotide or amino acid substitution for phylogenetic analysis. | View Modeltest NG |
| Mricron | Biology | MRI image viewer and analysis software tool. | View Mricron |
| Nanosim | Biology | Nanosim is a simulation tool for nanopore sequencing. | View Nanosim |
| NextDenovo | Biology | NextDenovo is a string graph-based de novo assembler for long reads | View NextDenovo |
| Nextpolish | Biology | NextPolish is a software for polishing long-read assemblies. | View Nextpolish |
| Pbsuite | Biology | PBsuite is a suite of bioinformatics tools for PacBio long-read sequencing data analysis. | View Pbsuite |
| Phylobayes | Biology | Bayesian inference of phylogenies from DNA/RNA data. | View Phylobayes |
| Poretally | Biology | Benchmark nanopore assembly pipelines using poreTally. | View Poretally |
| Price | Biology | Price is a de novo genome assembler. | View Price |
| pyRad | Biology | pyRAD: Python-based restriction site associated DNA analysis. | View pyRad |
| Racer | Biology | Hybrid assembly correction tool for long reads. | View Racer |
| Racon | Biology | Racon is a consensus module for long-read assemblers. | View Racon |
| Redundans | Biology | Redundans: reduce redundancy and improve genome assembly. | View Redundans |
| Sga | Biology | SGA: de Bruijn graph-based genome assembly tool. | View Sga |
| SPAdes | Biology | SPAdes: de novo assembly of microbial genomes. | View SPAdes |
| Sra toolkit | Biology | NCBI SRA file format conversion and manipulation tool. | View Sra toolkit |
| Star | Biology | Star is a fast RNA-seq aligner. | View Star |
| Velvet | Biology | Velvet is a de novo short read assembler. | View Velvet |
| Boost | Utilities | Portable source-level C++ libraries and development tools. | View Boost |
| Charm ++ | Utilities | Parallel programming system with dynamic load balancing. | View Charm ++ |
| HPC Compilers | Utilities | Collection of installed compilers on HPC | View HPC Compilers |
| Cuda | Utilities | Parallel computing platform and programming model developed by NVIDIA | View Cuda |
| Eigen | Utilities | C++ template library for linear algebra | View Eigen |
| Go | Utilities | Open source programming language for networked computing. | View Go |
| Gsl | Utilities | C library for numerical computations and statistics. | View Gsl |
| Julia | Utilities | High-level dynamic programming language for technical computing. | View Julia |
| NetCDF | Utilities | Data format and software for scientific data access. | View NetCDF |
| Perl | Utilities | High-level scripting language for text manipulation. | View Perl |
| Pgi | Utilities | High-performance optimizing compilers for parallel computing. | View Pgi |
| Ruby | Utilities | Dynamic, open source programming language with elegance. | View Ruby |
| Singularity | Utilities | Containerization platform for scientific and high-performance computing. | View Singularity |
| Spark | Utilities | Distributed computing system for big data processing. | View Spark |
| Valgrind | Utilities | Dynamic analysis tools for debugging and profiling. | View Valgrind |
| Conda | Utilities | Package manager for Python (and more). | View Conda |
| TCL/TK | Utilities | TCL/TK: GUI development with easy scripting language. | View TCL/TK |
| Trimgalore | Biology | Adapter trimming tool for next-gen sequencing data. | View Trimgalore |
| WRF-Hydro | GIS | Hydrological modeling system for simulating water cycle. | View WRF-Hydro |
| Udunits | Utilities | Library for handling units of physical quantities. | View Udunits |
| VCF Tools | Biology | Utility for manipulating variant call format files. | View VCF Tools |