HPC Software Info

Many popular software packages including compilers are installed and available as modules on LCC. For some software and compilers, different versions are available and you can use an older version if you specify the version. The default in most cases is the latest version.

On LCC, this is very important because the compiler version selection can affect how the application runs or performs. Projects that were built on our older cluster such as DLX2/3 may need to be recompiled for LCC.

You may send the request to help-hpc@hpc.uky.edu that applications be installed.

Installed Software

Note:

The following list could be incomplete because of the frequent new software requests on LCC.
The current list of modules is available on each login node
Type: "module avail"
You can load software available as a module
Type: "module load software name"
"module unload software name" to unload the module
To find detailed information about a particular package you
must specify the version if there is more than one version:
for example: "module spider software/1.1"

Search by Software Name:

Software	Short Description
Abyss	Parallel assembler for short read sequence data
ADMIXTURE	UCLA Human Genetics Software Distribution
AMBER	A suite of biomolecular simulation programs
AMBER tools	Consists of several independently developed packages that work with AMBER
Anaconda	A platform for data science and machine learning
Ansys	Licensed: General purpose finite element modeling package
Ansys/fluids	Comprehensive product suite for modeling fluid
Ansys/structures	Ansys structural analysis software enables you to solve complex structural engineering problems
ArrayFire	High-performance software library designed to help run code faster
ASE	Set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing
Augustus	A program that predicts genes in eukaryotic genomic sequences.
Augustus-braker	Pipeline for fully automated prediction of protein-coding gene structures
autodock_vina-1.1.2	Docking software
Automake	A tool for automatically generating Makefile.in files compliant with the GNU Coding Standards.
Bcftools	A set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF
bcl2fastq2	A software that demultiplexes sequencing data and converts BCL files into FASTQ files.
beagle-lib	General-purpose library for evaluating the likelihood of sequence evolution on trees
beast	Bayesian analysis of molecular sequences
bedtools	A powerful toolset for genome arithmetic
bioconductor-ChAMP	Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
bioconductor-DESeq	Differential gene expression analysis based on the negative binomial distribution
bioconductor-edgeR	Empirical Analysis of Digital Gene Expression Data in R
Blast	A search tool that finds regions of local similarity between nucleotide or protein sequences
Blat	Alignment tool like BLAST, but structured differently
bonito-0.0.8	Convolution Basecaller for Oxford Nanopore Reads
Boost	Peer-reviewed C++ source libraries
Bowtie	Ultrafast, memory-efficient short read aligner. See related tool Bowtie2
bpp	Bayesian analysis of genomic sequence data under the multispecies coalescent model
BRAKER	Pipeline for fully automated prediction of protein-coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes
BUSCO	From QC to gene prediction and phylogenomics
BWA	A fast light-weight tool that aligns relatively short sequences to a sequence database
Canu	Fork of the Celera Assembler designed for high-noise single-molecule sequencing
CD-HIT	Program for clustering and comparing protein or nucleotide sequences
Cell Ranger	Analysis pipelines that process Chromium single-cell RNA-seq
CHARMM	A molecular simulation program
CrossMap	Provides convenient conversion of genome coordinates between different assemblies, also known as a liftover
Cuda	A parallel computing platform and application programming interface model created by Nvidia.
Cufflinks	Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Cutadapt	Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequences from your high-throughput sequencing reads.
deep-md	A deep learning package for many-body potential energy representation and molecular dynamics (CPU and GPU)
Diamond	Alignment tool for aligning short DNA sequencing reads to a protein reference database
dispy	Distributed and Parallel Computing with/for Python
dock6	Molecular modeling program used to identify potential binding geometries and interactions of a molecule to a target.
Eigen	high-level C++ library of template headers
Ensembl-vep-99.2	Toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions.
Exonerate	A generic tool for sequence comparison
FastQC	Quality control tool for high throughput sequence data
FEniCS	Computing platform for solving partial differential equations
FFTW	Fast Fourier transforms. Ocelote has multiple versions
GAMESS	The General Atomic and Molecular Electronic Structure System
GATK	Genome analysis toolkit
Gaussian	Electronic structure program.
Gizmo	A flexible, massively-parallel, multi-physics simulation code.
Gmsh	An open-source 3D finite element mesh generator with a built-in CAD engine and post-processor.
Gromacs	Molecular dynamics software primarily designed for biomolecular systems
GSL	The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers
HDF5	Data model, library, and file format for storing and managing data
HISAT2	Graph-based alignment of next-generation sequencing reads to a population of genomes
HTSeq	Analyzing high-throughput sequencing data with Python
HyPhy	Hypothesis testing using Phylogenies
impi	Intel MPI Library (C/C++/Fortran for x86_64)
Intel Compilers	Intel licensed compilers
intelpython3_full	Intel Distribution for Python
ipyrad	An interactive assembly and analysis toolkit for restriction-site associated DNA (RAD-seq) and related data types.
Java	Programming language
JellyFish	Fast, memory-efficient counting of k-mers in DNA. Used by Trinity
jmodeltest	A tool to carry out a statistical selection of best-fit models of nucleotide substitution
Julia	High-level, high-performance dynamic programming language for technical computing
kallisto	A program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
Lammps	Molecular dynamics code
Libtool	The GNU Portable Library Tool
Lumerical	High-Performance Photonic Simulation Software
MACS2	Model-based Analysis of ChIP-Seq
make	A tool which controls the generation of executables and other non-source files of a program from the program's source files
Maker	Portable and easily configurable genome annotation pipeline
Maple	Math software that combines the world's most powerful math engine with an interface
MapSplice	Software for mapping RNA-seq data to reference genome for splice junction discovery that depends only on the reference genome, and not on any further annotations
MashMap	A fast approximate aligner for long DNA sequences
MATLAB	High-level language and interactive environment perform computationally intensive tasks
matplotlib	A comprehensive library for creating static, animated, and interactive visualizations in Python.
Meryl	A genomic k-mer counter (and sequence utility) with nice features
meshio-4.0.9	Input/output for many mesh formats
migrate-n	Software that estimates population parameters, effective population sizes and migration rates of n populations, using genetic data
Miniconda3	A free minimal installer for conda
minimap2	A versatile pairwise aligner for genomic and spliced nucleotide sequences
Molpro	Quantum Chemistry Software
mono	A project to create an Ecma standard-compliant. NET Framework-compatible software framework
mothur	A single resource to analyze molecular data that is used by microbial ecologists
mpi4py	MPI for Python
MrBayes	A program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
MultiQC	A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
NAMD	Parallel molecular dynamics code designed for HPC simulation of large biomolecular systems
NetworkX	A Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
NextFlow	Data-driven computational pipelines
NOTUNG	A gene tree-species tree reconciliation software package that supports duplication-loss (DL) and duplication-transfer-loss (DTL) event models with a parsimony-based optimization criterion.
NumPy	The fundamental package for scientific computing with Python
NWChem	Open Source High-Performance Computational Chemistry
OpenMPI	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.
OpenSees	The Open System for Earthquake Engineering Simulation
ORCA	An ab initio, DFT and semiempirical SCF-MO package
OrthoFinder	Phylogenetic orthology inference for comparative genomics
ParaView	An open-source, multi-platform data analysis and visualization application.
Perl	Programming language
PGI	PGI compilers and tools
pgi-cuda	PGI Cuda Fortran Compiler
phyluce	A software package that was initially developed for analyzing data collected from ultraconserved elements in organismal genomes
Picard	A set of command-line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Pilon	A software tool used for automatically improve draft assemblies and find variation among strains
Plink	Genome association analysis toolset
PLUMED	Community-developed library that provides a wide range of different methods, which include: enhanced-sampling algorithms
PRANK-170427	A probabilistic multiple sequence alignment program for DNA, codon and amino-acid sequences
proovread	Consists of a hybrid correction pipeline for single-molecule real-time single-molecule, real-time (SMRT) reads
Python	Object-oriented programming language
Qiime2	Next-generation microbiome bioinformatics platform
QuantumEspresso	An integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale.
R	Programming language for statistics analysis
R-SaTScan	A powerful stand-alone software program that runs spation-temporal scan statistics.
RAxML	A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion
RAxML-NG	RAxML Next Generation (Successor of RAxML)
Rsem	RNA-Seq by Expectation-Maximization
Samtools	A suite of programs for interacting with high-throughput sequencing data
SAS	Suite developed by SAS Institute for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics.
SciPy	A python-based ecosystem of software for mathematics, science, and engineering
Shasta	Long read assembler
Singularity	Containers let users package their scientific workflows, software libraries, and data
SpliceV	Visualize coverage, canonical, and backsplice junctions.
SRA toolkit	Collection of tools and libraries for using data in the INSDC Sequence Read Archives
Stacks	Software pipeline for building loci from short-read sequences
Star	RNA-seq Aligner
StringTie	Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts
Structure	Software for population genetics inference
Subread	Software programs for processing next-gen sequencing read data
TelSeq	software that estimates telomere length from whole-genome sequencing data (BAMs).
tk	Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches.
TopHat	Fast splice junction mapper for RNA-Seq reads
TotalView	HPC debugging software
Trim Galore	A wrapper tool around Ctadapt and FastQC, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
Trinity	A package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data
Trinotate	Annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.
ucsc-fatotwobit	Convert DNA from fasta to 2bit format
VASP	Atomic-scale materials modeling
VCFtools	Tool provide easily accessible methods for working with complex genetic variation data in the form of VCF files
WhatsHap	software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly.