Skip to main content

Below is a list of software available on BisonNet. Most software packages are added and removed from your environment using Environment Modules (e.g. module load matlab). If you need additional software, please submit a request by emailing bisonnet@bucknell.edu.

Also, some software packages have specific instructions that are necessary to follow.

SoftwareVersionDescriptionModule
augustus3.5.0Predicts genes in eukaryotic genomic sequencesassembly_assessment
bamtools2.5.2Manipulate BAM (genetic sequence) filesassembly_assessment
BBTools35.85BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence dataassembly_assessment
BCFTools1.21BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCFbcftools
bedtools22.31.1Manipulate bed format filesseq_tools
bowtie22.5.4Map reads to a reference genomealignment (python/3.12-bio)
Bracken3.0.1Bayesian Reestimation of Abundance with KrakENkraken2
Braker33.0.8BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomesbraker3
BUSCO5.8.3Measures quality of assemblyassembly_assessment (python/3.12-bio)
canu2.3A single molecule sequence assembler for genomes large and small.
assembly
chromap0.2.7Fast alignment and preprocessing of chromatin profilesgenome
COMSOL Multiphysics6.3A finite element analysis, solver and multiphysics simulation softwarecomsol
CUDA12.6.3The NVIDIA® CUDA® Toolkit provides a development environment for creating high performance GPU-accelerated applications.cuda
cudnn9.8.0The NVIDIA CUDA® Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.cudnn
dfam-tetools2025.03.26Dfam Transposable Element Tools singularity container
dfam-tetools
dvr-scan1.7Find and extract motion events in videos.python/3.10-misc
emacs30.1GNU Emacs editoremacs
EMBOSS6.6.0Manipulating sequence files, among other thingsseq_tools
EVidence Modeler2.1.0The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structuresannotation
exonerate2.4.0Exonerate is a generic tool for pairwise sequence comparisonexonerate (python/3.12-bio)
fasta-splitter.pl0.2.7Split FASTA filesseq_tools
fastp0.24.0A tool designed to provide fast all-in-one preprocessing for FastQ files.fastp,qc
fastQC0.12.1To assess the quality of DNA sequence dataqc
fastx_toolkit0.0.14To perform basic manipulations on DNA sequence dataqc
ffmpeg7.1AV conversion toolsffmpeg
funannotate1.8.5Funannotate is a genome prediction, annotation, and comparison software packagepython/3.12-bio
Gaussian16.B.01Computational chemistrygaussian
gcc/g++/gfortran11.5.0Open source compiler collection(none required)
GCTA1.94.3Genome-wide Complex Trait Analysisseq_tools
gmap-gsnap2024-11-20GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and
GSNAP: Genomic Short-read Nucleotide Alignment Program
alignment
GT-POWER2025.1.0001GT-POWER is used to predict engine performance quantities such as power, torque, airflow, volumetric efficiency, fuel consumption, turbocharger performance and matching, and pumping losses, to name just a few.GT-POWER
Gurobi Optimizer12.0.1An optimization solver for linear programming (LP), quadratic programming (QP), quadratically constrained programming (QCP), mixed integer linear programming (MILP), mixed-integer quadratic programming (MIQP), and mixed-integer quadratically constrained programming (MIQCP)gurobi-optimizer
HISAT22.2.1graph-based alignment of next generation sequencing reads to a population of genomesalignment
hmmer3.4Used for searching sequence databases for sequence homologs and for making sequence alignmentsassembly_assessment
HTStream1.3.0Quality control pipeline for High Throughput Sequencing dataqc
IBAMR0.16An adaptive and distributed-memory parallel implementation of the immersed boundary (IB) method(not a module)
ILOG CPLEX Studio22.1.2A mathematical optimization software packageCPLEX
insectOR2024.05.09This package helps to annotate genes coding for any specific family of proteins from a medium sized genomeinsectOR
ipyrad0.9.104Assembly and analysis of RAD-seq type genomic data setsradseq (python/3.12-bio)
iqtree2.4.0Build phylogenetic trees from sequencesphylogeny
I-TASSER5.2Iterative Threading ASSEmbly RefinementI-TASSER
JDFTx1.7.0JDFTx is a plane-wave density-functional theory (DFT) code designed to be as easy to develop with as it is easy to use.jdftx
jellyfish2.3.1Tool for fast, memory-efficient counting of k-mers in DNAalignment
jmodeltest22.1.10Find the best model of sequence evolution for building phylogeniesphylogeny
kallisto0.51.1Map reads to a reference genome (without sketchiness)alignment
Kraken22.1.4A taxonomic classification systemkraken2
LAMMPS2024.08.29LAMMPS is a classical molecular dynamics code with a focus on materials modeling.lammps
MAFFT7.471Align sequencesmafft
Maker3.01.03MAKER is a portable and easily configurable genome annotation pipeline.annotation
Mathematica14.2.1A modern technical computing system spanning most areas of technical computing — including neural networks, machine learning, image processing, geometry, data science, visualizations, and others.mathematica
MatlabR2024bMulti-paradigm numerical computing environment and programming languagematlab
metaeuk7.0Sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomicsassembly_assessment
minimap22.28A versatile pairwise aligner for genomic and spliced nucleotide sequencesgenome
MrBayes3.2.7Building phylogeniesphylogeny
MultiQC1.28Aggregate results from bioinformatics analyses across many samples into a single reportpython/3.12-bio
ncbi-BLAST+2.16.0+BLAST alignment to database. $NCBI_DATA set to top-level of weekly database downloads.ncbi_blast
NextPolish1.4.1Fast and accurately polish the genome generated by long reads.genome
octave9.4.0Powerful mathematics-oriented syntax with built-in 2D/3D plotting and visualization toolsoctave
Omni-C2025.03.25The Dovetail™ Omni-C™ library uses a sequence-independent endonuclease for chromatin digestion prior to proximity ligation and library generation.Omni-C
OpenCV4.11.0Open source Computer Visionopencv
openmpi5.0.7Message Passing Interface project, generally used for running parallel code.openmpi
ORCA6.0.1ORCA is a powerful and versatile quantum chemistry software package.orca
PAL2NAL14.1Force nucleotides onto protein alignmentsalignment (python/3.12-bio)
PAML4.10.7Testing genes for selectionmolecular_evolution
PASTEC2025.04.11Singularity image for PASTEC (transposable elements classification tool).repeats
Perl5.40.1General purpose programming languageperl
plink1.9PLINK is a free, open-source whole genome association analysis toolsetplink
prodigal2.6.3Prodigal Gene Prediction Softwareassemsbly_assessment
purge_dups1.2.6haplotypic duplication identification toolgenome
Python3.12General purpose programming languagepython
pysam0.22.1Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files.python/3.12-bio
PySPH1.0b2.dev0A framework for Smoothed Particle Hydrodynamics in Pythonpython/3.10-misc
R4.4.3Software environment for statistical computing and graphicsR
RELION5.0relion (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a software package that employs an empirical Bayesian approach for electron cryo-microscopy (cryo-EM) structure determination.RELION
RSEM1.3.3Calculates read counts from BAM filesalignment
salmon1.10.0Map reads to a reference genome (wicked fast)alignment
samtools1.16.1Manipulate sam and bam filesseq_tools,genome
Scaff10X5.0Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-readsassembly
seqtk1.4Toolkit for processing sequences in FASTA/Q formatsseq_tools
SIMULIA2025Software suite, including Abaqus and Tosca, for finite element analysis and computer-aided engineeringSIMULIA
SOAP DeNovor242Assembling genomesassembly
SRA_Toolkit3.2.1Downloads files from the Sequence Read Archiveseq_tools
STAR2.7.11bMap reads to a reference genomealignment
TEClass2.1.3bClassification of TE consensus sequencesrepeats
TOGA1.1.7TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes.genome
TopHat2.1.1TopHat is a fast splice junction mapper for RNA-Seq reads.alignment
TransDecoder5.7.1Identifies candidate coding regions within transcript sequencestransdecoder
Trimmomatic0.39To trim bad quality sequence dataqc
Trinity2.15.2For transcriptome assemblyTrinity
vcflib1.0.13

Aboutpython/3.12-bio
vcftools0.1.16C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindingsseq_tools
VEP113.4Variant Effect Predictorseq_tools
wtgbg22.5A fuzzy Bruijn graph approach to long noisy reads assemblygenome
XCrySDen1.6.2XCrySDen is a crystalline and molecular structure visualisation programxcrysden
xmgrace5.1.252D plotting toolxmgrace
yahs1.2.2Yet another Hi-C scaffolding toolgenome