Software
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.
| Software | Version | Description | Module |
|---|---|---|---|
| admixture | 1.3.0 | A software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. | admixture |
| augustus | 3.5.0 | Predicts genes in eukaryotic genomic sequences | assembly_assessment |
| avogadro2 | 1.100 | A free and open source molecular editor and visualization tool. | avogadro2 |
| bamtools | 2.5.2 | Manipulate BAM (genetic sequence) files | assembly_assessment |
| BBTools | 35.85 | BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data | assembly_assessment |
| BCFTools | 1.21 | BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF | bcftools |
| bedtools2 | 2.31.1 | Manipulate bed format files | seq_tools |
| BLAST | 2.2.26 | BLAST finds regions of similarity between biological sequences. Note that this is the legacy C tookit BLAST and should only be used as required by other programs. Generally, most people should use BLAST+, which is part of the ncbi-blast module. | blast |
| bowtie2 | 2.5.4 | Map reads to a reference genome | alignment (python/3.12-bio) |
| Bracken | 3.0.1 | Bayesian Reestimation of Abundance with KrakEN | kraken2 |
| Braker3 | 3.0.8 | BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes | braker3 |
| BUSCO | 5.8.3 | Measures quality of assembly | assembly_assessment (python/3.12-bio) |
| canu | 2.3 | A single molecule sequence assembler for genomes large and small. | assembly |
| chromap | 0.2.7 | Fast alignment and preprocessing of chromatin profiles | genome |
| COMSOL Multiphysics | 6.3 | A finite element analysis, solver and multiphysics simulation software | comsol |
| CUDA | 12.6.3 | The NVIDIA® CUDA® Toolkit provides a development environment for creating high performance GPU-accelerated applications. | cuda |
| cudnn | 9.8.0 | The NVIDIA CUDA® Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. | cudnn |
| dfam-tetools | 2025.03.26 | Dfam Transposable Element Tools singularity container | dfam-tetools |
| dvr-scan | 1.7 | Find and extract motion events in videos. | python/3.10-misc |
| emacs | 30.1 | GNU Emacs editor | emacs |
| EMBOSS | 6.6.0 | Manipulating sequence files, among other things | seq_tools |
| EVidence Modeler | 2.1.0 | The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures | annotation |
| exonerate | 2.4.0 | Exonerate is a generic tool for pairwise sequence comparison | exonerate (python/3.12-bio) |
| fasta-splitter.pl | 0.2.7 | Split FASTA files | seq_tools |
| fastp | 0.24.0 | A tool designed to provide fast all-in-one preprocessing for FastQ files. | fastp,qc |
| fastQC | 0.12.1 | To assess the quality of DNA sequence data | qc |
| fastx_toolkit | 0.0.14 | To perform basic manipulations on DNA sequence data | qc |
| ffmpeg | 7.1 | AV conversion tools | ffmpeg |
| funannotate | 1.8.5 | Funannotate is a genome prediction, annotation, and comparison software package | python/3.12-bio |
| Gaussian | 16.B.01 | Computational chemistry | gaussian |
| gcc/g++/gfortran | 11.5.0 | Open source compiler collection | (none required) |
| GCTA | 1.94.3 | Genome-wide Complex Trait Analysis | seq_tools |
| glimmer | 3.02 | Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. | glimmer |
| gmap-gsnap | 2024-11-20 | GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program | alignment |
| GT-POWER | 2025.1.0001 | GT-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 Optimizer | 12.0.1 | 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 |
| HISAT2 | 2.2.1 | graph-based alignment of next generation sequencing reads to a population of genomes | alignment |
| hmmer | 3.4 | Used for searching sequence databases for sequence homologs and for making sequence alignments | assembly_assessment |
| HTStream | 1.3.0 | Quality control pipeline for High Throughput Sequencing data | qc |
| IBAMR | 0.16 | An adaptive and distributed-memory parallel implementation of the immersed boundary (IB) method | (not a module) |
| ILOG CPLEX Studio | 22.1.2 | A mathematical optimization software package | CPLEX |
| insectOR | 2024.05.09 | This package helps to annotate genes coding for any specific family of proteins from a medium sized genome | insectOR |
| ipyrad | 0.9.104 | Assembly and analysis of RAD-seq type genomic data sets | radseq (python/3.12-bio) |
| iqtree | 2.4.0 | Build phylogenetic trees from sequences | phylogeny |
| I-TASSER | 5.2 | Iterative Threading ASSEmbly Refinement | I-TASSER |
| JDFTx | 1.7.0 | JDFTx is a plane-wave density-functional theory (DFT) code designed to be as easy to develop with as it is easy to use. | jdftx |
| jellyfish | 2.3.1 | Tool for fast, memory-efficient counting of k-mers in DNA | alignment |
| jmodeltest2 | 2.1.10 | Find the best model of sequence evolution for building phylogenies | phylogeny |
| kallisto | 0.51.1 | Map reads to a reference genome (without sketchiness) | alignment |
| Kraken2 | 2.1.4 | A taxonomic classification system | kraken2 |
| LAMMPS | 2024.08.29 | LAMMPS is a classical molecular dynamics code with a focus on materials modeling. | lammps |
| MAFFT | 7.471 | Align sequences | mafft |
| Maker | 3.01.03 | MAKER is a portable and easily configurable genome annotation pipeline. | annotation |
| Mathematica | 14.2.1 | A modern technical computing system spanning most areas of technical computing — including neural networks, machine learning, image processing, geometry, data science, visualizations, and others. | mathematica |
| Matlab | R2024b | Multi-paradigm numerical computing environment and programming language | matlab |
| metaeuk | 7.0 | Sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics | assembly_assessment |
| minimap2 | 2.28 | A versatile pairwise aligner for genomic and spliced nucleotide sequences | genome |
| MrBayes | 3.2.7 | Building phylogenies | phylogeny |
| MultiQC | 1.28 | Aggregate results from bioinformatics analyses across many samples into a single report | python/3.12-bio |
| ncbi-BLAST+ | 2.16.0+ | BLAST alignment to database. $NCBI_DATA set to top-level of weekly database downloads. | ncbi-blast |
| NextPolish | 1.4.1 | Fast and accurately polish the genome generated by long reads. | genome |
| octave | 9.4.0 | Powerful mathematics-oriented syntax with built-in 2D/3D plotting and visualization tools | octave |
| Omni-C | 2025.03.25 | The Dovetail™ Omni-C™ library uses a sequence-independent endonuclease for chromatin digestion prior to proximity ligation and library generation. | Omni-C |
| OpenCV | 4.11.0 | Open source Computer Vision | opencv |
| openmpi | 5.0.7 | Message Passing Interface project, generally used for running parallel code. | openmpi |
| ORCA | 6.0.1 | ORCA is a powerful and versatile quantum chemistry software package. | orca |
| PAL2NAL | 14.1 | Force nucleotides onto protein alignments | alignment (python/3.12-bio) |
| PAML | 4.10.7 | Testing genes for selection | molecular_evolution |
| PASTEC | 2025.04.11 | Singularity image for PASTEC (transposable elements classification tool). | repeats |
| Perl | 5.40.1 | General purpose programming language | perl |
| PfamScan | 1.6 | PfamScan is used to search a FASTA sequence against a library of Pfam HMM. | pfamscan |
| plink | 1.9 | PLINK is a free, open-source whole genome association analysis toolset | plink |
| prodigal | 2.6.3 | Prodigal Gene Prediction Software | assemsbly_assessment |
| purge_dups | 1.2.6 | haplotypic duplication identification tool | genome |
| Python | 3.12 | General purpose programming language | python |
| pysam | 0.22.1 | Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. | python/3.12-bio |
| PySPH | 1.0b2.dev0 | A framework for Smoothed Particle Hydrodynamics in Python | python/3.10-misc |
| R | 4.4.3 | Software environment for statistical computing and graphics | R |
| RELION | 5.0 | relion (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 |
| RSEM | 1.3.3 | Calculates read counts from BAM files | alignment |
| salmon | 1.10.0 | Map reads to a reference genome (wicked fast) | alignment |
| samtools | 1.16.1 | Manipulate sam and bam files | seq_tools,genome |
| Scaff10X | 5.0 | Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads | assembly |
| seqtk | 1.4 | Toolkit for processing sequences in FASTA/Q formats | seq_tools |
| SIMULIA | 2025 | Software suite, including Abaqus and Tosca, for finite element analysis and computer-aided engineering | SIMULIA |
| SOAP DeNovo | r242 | Assembling genomes | assembly |
| SRA_Toolkit | 3.2.1 | Downloads files from the Sequence Read Archive | seq_tools |
| stacks | 2.68 | Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform | stacks |
| STAR | 2.7.11b | Map reads to a reference genome | alignment |
| structure | 2.3.4 | A free software package for using multi-locus genotype data to investigate population structure. | structure |
| TEClass | 2.1.3b | Classification of TE consensus sequences | repeats |
| TOGA | 1.1.7 | TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. | genome |
| TopHat | 2.1.1 | TopHat is a fast splice junction mapper for RNA-Seq reads. | alignment |
| TransDecoder | 5.7.1 | Identifies candidate coding regions within transcript sequences | transdecoder |
| Trimmomatic | 0.39 | To trim bad quality sequence data | qc |
| Trinity | 2.15.2 | For transcriptome assembly | Trinity |
| vcflib | 1.0.13 | C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings | python/3.12-bio |
| vcftools | 0.1.16 | C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings | seq_tools |
| VEP | 113.4 | Variant Effect Predictor | seq_tools |
| Visual Studio Code | 1.100.3 | Integrated development environment | vscode |
| wtgbg2 | 2.5 | A fuzzy Bruijn graph approach to long noisy reads assembly | genome |
| XCrySDen | 1.6.2 | XCrySDen is a crystalline and molecular structure visualisation program | xcrysden |
| xmgrace | 5.1.25 | 2D plotting tool | xmgrace |
| yahs | 1.2.2 | Yet another Hi-C scaffolding tool | genome |