Beartooth Software List

Overview

Herein, find summaries of each package with links to a more detailed page for each package.
Below is a list of software / applications that are available on Beartooth. Click the software title to learn more about a particular software package, including its associated module name that can be used to find available versions and to load.
Please refer to our LMOD page for information about and how to use the module system:

Last Updated: 5/29/24

application

compiler

GNU

Intel oneAPI

NVidia HPC SDK

containers and virtual envs

Micromamba	Miniconda	Miniforge
Singularity

ide

PyCharm

RStudio

language

C/C++	Fortran	Go
Java	Julia	Perl
Python	R	Ruby
Rust

libraries and toolkits

Adios2	Bedops	BioPerl
BioPython	CGAL	Cuda
cuDNN	ELPA	FASTX-Toolkit
GDAL	GEOS	GSL
NCO	NetCDF	OpenBLAS
OpenMPI	PETSc	Rmpi
SRA-Toolkit

We haves 100s of libraries and do not have a wiki page for them all. Popular libraries also include: boost, expat, fftw, gmp, hdf5, hypre, motif, netlib-lapack, netcdf-c/cxx4, netlib-scalapack, openblas, parmetis, scotch, udunits, wannier90 and zoltan to list just a few. We recommend, once you have access, to perform a module spider to see if it is installed, but not listed above.

utility

Ant	Aspera-Connect	CMake
FileZilla	Gffcompare	Git
GNUPlot	GSUtil	IOR
KentUtils	NCBI-Datasets-CLI	newick_util
PAPI	Parallel (gnu)	Ranger
RClone	Sequence Hub CLI	Snakemake
Subversion

There are 10s of utilities that will be automatically available on the System as part of the OS without needing to load a module: For example: bzip2, curl, tar…
Some utilities will come as part of the system but might have a module with a newer version: For example: gmake

Alphafold	Amber	ANGSD
ATAT	Augustus	BamTools
Bayescan	BCFtools	Beast2
Bedtools2	Blast+	Blender
Brains	Busco	BWA
Canu	CDNest	Cell Ranger ATAC
Circlator	Clustal Omega	Cmdstan
Cutadapt	DFTB	EddyProEngine
EnergyPlus	Ensembl VEP	Exonerate
FastQC	Freebayes	FunGAP
GATK	Gaussian & GaussView	GeneMark-ES Suite
GrADS	Grenedalf	Gromacs
Hifiasm	HISAT2	HTSeq
HTSlib	HyDe	IDL
IGV	ImageJ	ImageMagick
Interproscan	IPA	IQ-Tree
Jags	Kallisto	Kraken
LAMMPS	LDhelmet	LocalColabFold
Localizer	Maestro	MAFFT
Maker	MATLAB	Metaxa2
MFiX	MOOSE	MSMC2
MultiQC	MUMmer4	NCBI-RMBlast
Nextflow	OpenFOAM.org	Orca
Packmol	ParaView	ParFlow
PathoFact	Paup	PGDSpider
Picard	Prodigal	Proovread
Qiime2	Quantum Espresso	RAxML
Ray	RepeatMasker	RoseTTAFold
Salmon	Samtools	SeqKit
SignalP	SLiM	Snap-korf
SourceTracker2	SPades	Star
StringTie	Structure	Trimmomatic
Trinity	USearch	VASP
VASPKIT	VCF2GWAS	VCFtools
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