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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 that applications be installed.

Installed Software


  • 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:

SoftwareShort Description
AbyssParallel assembler for short read sequence data
ADMIXTUREUCLA Human Genetics Software Distribution
AMBERA suite of biomolecular simulation programs
AMBER toolsConsists of several independently developed packages that work with AMBER
AnacondaA platform for data science and machine learning
AnsysLicensed: General purpose finite element modeling package
Ansys/fluidsComprehensive product suite for modeling fluid
Ansys/structuresAnsys structural analysis software enables you to solve complex structural engineering problems
ArrayFireHigh-performance software library designed to help run code faster
ASESet of tools and Python modules for setting up, manipulating, running, visualizing and analyzing
AugustusA program that predicts genes in eukaryotic genomic sequences.
Augustus-brakerPipeline for fully automated prediction of protein-coding gene structures
autodock_vina-1.1.2Docking software
AutomakeA tool for automatically generating files compliant with the GNU Coding Standards.
BcftoolsA set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF
bcl2fastq2A software that demultiplexes sequencing data and converts BCL files into FASTQ files.
beagle-libGeneral-purpose library for evaluating the likelihood of sequence evolution on trees
beastBayesian analysis of molecular sequences
bedtoolsA powerful toolset for genome arithmetic
bioconductor-ChAMPChip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
bioconductor-DESeqDifferential gene expression analysis based on the negative binomial distribution
bioconductor-edgeREmpirical Analysis of Digital Gene Expression Data in R
BlastA search tool that finds regions of local similarity between nucleotide or protein sequences
BlatAlignment tool like BLAST, but structured differently
bonito-0.0.8Convolution Basecaller for Oxford Nanopore Reads
BoostPeer-reviewed C++ source libraries
BowtieUltrafast, memory-efficient short read aligner. See related tool Bowtie2
bppBayesian analysis of genomic sequence data under the multispecies coalescent model
BRAKERPipeline for fully automated prediction of protein-coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes
BUSCOFrom QC to gene prediction and phylogenomics
BWAA fast light-weight tool that aligns relatively short sequences to a sequence database
CanuFork of the Celera Assembler designed for high-noise single-molecule sequencing
CD-HITProgram for clustering and comparing protein or nucleotide sequences
Cell RangerAnalysis pipelines that process Chromium single-cell RNA-seq
CHARMMA molecular simulation program
CrossMapProvides convenient conversion of genome coordinates between different assemblies, also known as a liftover
CudaA parallel computing platform and application programming interface model created by Nvidia.
CufflinksAssembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
CutadaptFinds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequences from your high-throughput sequencing reads.
deep-mdA deep learning package for many-body potential energy representation and molecular dynamics (CPU and GPU)
DiamondAlignment tool for aligning short DNA sequencing reads to a protein reference database
dispyDistributed and Parallel Computing with/for Python
dock6Molecular modeling program used to identify potential binding geometries
and interactions of a molecule to a target.
Eigenhigh-level C++ library of template headers
Ensembl-vep-99.2Toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions.
ExonerateA generic tool for sequence comparison
FastQCQuality control tool for high throughput sequence data
FEniCSComputing platform for solving partial differential equations
FFTWFast Fourier transforms. Ocelote has multiple versions
GAMESSThe General Atomic and Molecular Electronic Structure System
GATKGenome analysis toolkit
GaussianElectronic structure program.
GizmoA flexible, massively-parallel, multi-physics simulation code.
GmshAn open-source 3D finite element mesh generator with a built-in CAD engine and post-processor.
GromacsMolecular dynamics software primarily designed for biomolecular systems
GSLThe GNU Scientific Library (GSL) is a numerical library for C and C++ programmers
HDF5Data model, library, and file format for storing and managing data
HISAT2Graph-based alignment of next-generation sequencing reads to a population of genomes
HTSeqAnalyzing high-throughput sequencing data with Python
HyPhyHypothesis testing using Phylogenies
impiIntel MPI Library (C/C++/Fortran for x86_64)
Intel CompilersIntel licensed compilers
intelpython3_fullIntel Distribution for Python
ipyradAn interactive assembly and analysis toolkit for restriction-site associated DNA (RAD-seq) and related data types.
JavaProgramming language
JellyFishFast, memory-efficient counting of k-mers in DNA. Used by Trinity
jmodeltestA tool to carry out a statistical selection of best-fit models of nucleotide substitution
JuliaHigh-level, high-performance dynamic programming language for technical computing
kallistoA program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
LammpsMolecular dynamics code
LibtoolThe GNU Portable Library Tool
LumericalHigh-Performance Photonic Simulation Software
MACS2Model-based Analysis of ChIP-Seq
makeA tool which controls the generation of executables and other non-source files of a program from the program's source files
MakerPortable and easily configurable genome annotation pipeline
MapleMath software that combines the world's most powerful math engine with an interface
MapSpliceSoftware 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
MashMapA fast approximate aligner for long DNA sequences
MATLABHigh-level language and interactive environment perform computationally intensive tasks
matplotlibA comprehensive library for creating static, animated, and interactive visualizations in Python.
MerylA genomic k-mer counter (and sequence utility) with nice features
meshio-4.0.9Input/output for many mesh formats
migrate-nSoftware that estimates population parameters, effective population sizes and migration rates of n populations, using genetic data
Miniconda3A free minimal installer for conda
minimap2A versatile pairwise aligner for genomic and spliced nucleotide sequences
MolproQuantum Chemistry Software
monoA project to create an Ecma standard-compliant. NET Framework-compatible software framework
mothurA single resource to analyze molecular data that is used by microbial ecologists
mpi4pyMPI for Python
MrBayesA program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
MultiQCA modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
NAMDParallel molecular dynamics code designed for HPC simulation of large biomolecular systems
NetworkXA Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
NextFlowData-driven computational pipelines
NOTUNGA 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.
NumPyThe fundamental package for scientific computing with Python
NWChemOpen Source High-Performance Computational Chemistry
OpenMPIThe 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.
OpenSeesThe Open System for Earthquake Engineering Simulation
ORCAAn ab initio, DFT and semiempirical SCF-MO package
OrthoFinderPhylogenetic orthology inference for comparative genomics
ParaViewAn open-source, multi-platform data analysis and visualization application.
PerlProgramming language
PGIPGI compilers and tools
pgi-cudaPGI Cuda Fortran Compiler
phyluceA software package that was initially developed for analyzing data collected from ultraconserved elements in organismal genomes
PicardA set of command-line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
PilonA software tool used for automatically improve draft assemblies and find variation among strains
PlinkGenome association analysis toolset
PLUMEDCommunity-developed library that provides a wide range of different methods, which include: enhanced-sampling algorithms
PRANK-170427A probabilistic multiple sequence alignment program for DNA, codon and amino-acid sequences
proovreadConsists of a hybrid correction pipeline for single-molecule real-time single-molecule, real-time (SMRT) reads
PythonObject-oriented programming language
Qiime2Next-generation microbiome bioinformatics platform
QuantumEspressoAn integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale.
RProgramming language for statistics analysis
R-SaTScanA powerful stand-alone software program that runs spation-temporal scan statistics.
RAxMLA phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion
RAxML-NGRAxML Next Generation (Successor of RAxML)
RsemRNA-Seq by Expectation-Maximization
SamtoolsA suite of programs for interacting with high-throughput sequencing data
SASSuite developed by SAS Institute for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics.
SciPyA python-based ecosystem of software for mathematics, science, and engineering
ShastaLong read assembler
SingularityContainers let users package their scientific workflows, software libraries, and data
SpliceVVisualize coverage, canonical, and backsplice junctions.
SRA toolkitCollection of tools and libraries for using data in the INSDC Sequence Read Archives
StacksSoftware pipeline for building loci from short-read sequences
StarRNA-seq Aligner
StringTieFast and highly efficient assembler of RNA-Seq alignments into potential transcripts
StructureSoftware for population genetics inference
SubreadSoftware programs for processing next-gen sequencing read data
TelSeqsoftware that estimates telomere length from whole-genome sequencing data (BAMs).
tkTk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches.
TopHatFast splice junction mapper for RNA-Seq reads
TotalViewHPC debugging software
Trim GaloreA wrapper tool around Ctadapt and FastQC, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
TrinityA package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data
TrinotateAnnotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.
ucsc-fatotwobitConvert DNA from fasta to 2bit format
VASPAtomic-scale materials modeling
VCFtoolsTool provide easily accessible methods for working with complex genetic variation data in the form of VCF files
WhatsHapsoftware for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly.

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