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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
augustus3.4.0Predicts genes in eukaryotic genomic sequencesassembly_assessment
bamtools2.5.2Manipulate BAM (genetic sequence) filesassembly_assessment
BBTools2023.02.06
BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence dataassembly_assessment
BCFTools1.17BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCFbcftools
Beast22.7.0BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.beast2
bedtools2.30.0Manipulate bed format filesseq_tools
BioPerl1.7.8Perl tools for bioinformatics, genomics, and life scienceseq_tools
bowtie22.5.1


Map reads to a reference genomealignment (python/3.10-bio)
bracken2.7Bayesian Reestimation of Abundance with KrakENkraken2
Braker22.1.5BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomesbraker2
BUSCO5.4.5
Measures quality of assemblyassembly_assessment (python/3.10-bio)
BUSCO-phylogenomics1/12/2021Utility script to construct species phylogenies using BUSCOsBUSCO-phylogenomics
canu2.2A single molecule sequence assembler for genomes large and small.
assembly
COMSOL Multiphysics6.2A finite element analysis, solver and multiphysics simulation softwarecomsol
CUDA11.6.2The NVIDIA® CUDA® Toolkit provides a development environment for creating high performance GPU-accelerated applications.CUDA
cudnn8.4.0The NVIDIA CUDA® Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.cudnn
DRAP1.92De novo RNA-seq Assembly PipelineDRAP
dvr-scan1.5.1Find and extract motion events in videos.python/3.10-misc
EMBOSS6.6Manipulating sequence files, among other thingsseq_tools
EVidence Modeler1.1.1The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structuresannotation
exonerate2.2.0Exonerate is a generic tool for pairwise sequence comparisonexonerate
fastp0.23.2A tool designed to provide fast all-in-one preprocessing for FastQ files.qc, fastp
faSomeRecords (python)Retrieve fasta sequences from a multi-fasta fileseq_tools
fasta-splitter.pl0.2.6Split FASTA filesseq_tools
FastQC0.11.9To assess the quality of DNA sequence dataqc
fastx-toolkit0.0.14To perform basic manipulations on DNA sequence dataqc
ffmpeg5.1AV conversion toolsffmpeg
Funannotate2021-01.12Funannotate is a genome prediction, annotation, and comparison software packagefunannotate
Gaussian16.B.01Computational chemistrygaussian
gcc/g++/gfortran8.5.0Open source compiler collection(none required)
GCTA1.94.1Genome-wide Complex Trait Analysisseq_tools
GMAP12/17/2021GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and
GSNAP: Genomic Short-read Nucleotide Alignment Program
alignment
GT-POWER2024GT-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 Optimizer10.0.1
An 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
HISAT22.2.1
graph-based alignment of next generation sequencing reads to a population of genomesalignment
hmmer3.3.2Used for searching sequence databases for sequence homologs and for making sequence alignmentsassembly_assessment
HTStream1.3.0Quality control pipeline for High Throughput Sequencing dataqc
IBAMR0.7.10.11.0An adaptive and distributed-memory parallel implementation of the immersed boundary (IB) method(not a module)
ILOG CPLEX Studio22.1.1
A mathematical optimization software packageCPLEX
insectOR2024-05-09This package helps to annotate genes coding for any specific family of proteins from a medium sized genomeinsectOR
ipyrad0.9.90
Assembly and analysis of RAD-seq type genomic data setsradseq (python/3.10-bio)
IQtree1.6.12Build phylogenetic trees from sequencesphylogeny
I-TASSER5.2Iterative Threading ASSEmbly RefinementI-TASSER
JAGS4.3.2JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.JAGS
javaJava SE Development Kitjava
jellyfish2.3.0Tool for fast, memory-efficient counting of k-mers in DNAalignment
jmodeltest22.1.10Find the best model of sequence evolution for building phylogeniesphylogeny
kallisto0.46.1
Map reads to a reference genome (without sketchiness)alignment
Kraken22.1.1
A taxonomic classification systemkraken2
LAMMPS Molecular Dynamics Simulator2022.09.02LAMMPS is a classical molecular dynamics code with a focus on materials modeling.lammps
MAFFT7.505Align sequencesalignment
magma2.27-4Magma is a software package designed for computations in algebra, number theory, algebraic geometry and algebraic combinatorics. magma
Maker3..01.03MAKER is a portable and easily configurable genome annotation pipeline.annotation
mash2.3Fast genome and metagenome distance estimation using MinHashmash
Mathematica13A modern technical computing system spanning most areas of technical computing — including neural networks, machine learning, image processing, geometry, data science, visualizations, and others.mathematica
MATLABR2024aMulti-paradigm numerical computing environment and programming languagematlab
metaeuk2023.02.06Sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomicsassembly_assessment
MrBayes3.2.7aBuilding phylogeniesphylogeny
MultiQC1.14Aggregate results from bioinformatics analyses across many samples into a single reportpython/3.10-bio
nbo6
2023-02-22NBO6 for Gaussiangaussian
ncbi-BLAST+2.13.0+
BLAST alignment to database. $NCBI_DATA set to top-level of weekly database downloads.ncbi-blast
Oases0.2.09De novo transcriptome assembler for very short readsassembly
Octave7.2.0Powerful mathematics-oriented syntax with built-in 2D/3D plotting and visualization toolsoctave
OpenCV4.6.0Open source Computer Visionopencv
openmpi4.1.4Message Passing Interface project, generally used for running parallel code.openmpi
PAL2NAL14Force nucleotides onto protein alignmentsalignment
PAML4.9jTesting genes for selectionmolecular_evolution
PARI/GP2.13.4
PARI/GP is a widely used computer algebra system designed for fast computations in number theorypari
PASA2.5.2PASA PipelinePASA
Perl5.36.0General purpose programming languageperl
plink1.90PLINK is a free, open-source whole genome association analysis toolsetplink
prodigal2.6.3Prodigal Gene Prediction Softwareassembly_assessment
pysam0.21.0Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files.python/3.10-bio

PySPH1.0b1
A framework for Smoothed Particle Hydrodynamics in Pythonpython/3.10-misc
Python3.10General purpose programming language (See modules list)python
R4.2.1Software environment for statistical computing and graphicsR
RELION4.0relion (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
Sage9.6SageMath is a free open-source mathematics software systemsage
salmon1.9.0
Map reads to a reference genome (wicked fast)alignment
samtools1.16.1
Manipulate sam and bam filesseq_tools
SAS9.4Statistical software suite for data management, advanced analytics, multivariate analysis, business intelligence, criminal investigation, and predictive analytics.SAS
Scaff10X5Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-readsassembly
seqtk1.3Toolkit for processing sequences in FASTA/Q formatsseq_tools
SIMULIA2022
Software suite, including Abaqus and Tosca, for finite element analysis and computer-aided engineeringSIMULIA
SOAP de novor242Assembling genomesassembly
SPAdes3.15.4It’s all about the viruses: new coronaSPAdes, rnaviralSPAdes and metaviralSPAdes pipelines.SPAdes
SRA_Toolkit3.0.0Downloads files from the Sequence Read Archiveseq_tools
stacks2.65Population genetics with RAD datastacks
STAR2.7.10Map reads to a reference genomealignment
stringtie2.2.1Transcript assembly and quantification for RNA-Seqassembly
Tensorflow2.12.0Maching learning platformpython/3.10-deeplearn
TensorRT8.4.3.1NVIDIA® TensorRT™, an SDK for high-performance deep learning inferenceTensorRT
TopHat2.1.1TopHat is a fast splice junction mapper for RNA-Seq reads.alignment
TransDecoder5.5.0Identifies candidate coding regions within transcript sequencestransdecoder
trimmomatic0.39To trim bad quality sequence dataqc
Trinity (singularity)2.13.2For transcriptome assemblyTrinity
Trinnotate4.0.0For transcriptome assembly annotationTrinotate
vcftools0.1.16Manipulate vcf filesseq_tools
Velvet1.2.10Sequence assembler for very short readsassembly
VEP107Variant Effect Predictorseq_tools
XCrySDen1.6.2XCrySDen is a crystalline and molecular structure visualisation programxcrysden
xmgrace5.1.252D plotting toolxmgrace