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 | fast ancestry estimation | admixture |
| augustus | 3.3.1 | Predicts genes in eukaryotic genomic sequences | assembly_assessment |
| bamtools | 2.5.1 | Manipulate BAM (genetic sequence) files | assembly_assessment |
| Beast2 | 2.6.6 | BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. | beast2 |
| bedtools | 2.27.1 | Manipulate bed format files | seq_tools |
| BioPerl | 1.007002 | Perl tools for bioinformatics, genomics, and life science | seq_tools |
| bowtie2 | 2.4.4 | Map reads to a reference genome | alignment |
| bracken | 2.5 | Bayesian Reestimation of Abundance with KrakEN | kraken2 |
| Braker2 | 2.1.5 | BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes | braker2 |
| BUSCO | 4.1.3 | Measures quality of assembly | assembly_assessment |
| BUSCO-phylogenomics | 2021-01-12 | Utility script to construct species phylogenies using BUSCOs | BUSCO-phylogenomics |
| canu | 1.8 | A single molecule sequence assembler for genomes large and small. | assembly |
| COMSOL Multiphysics | 5.6 | A finite element analysis, solver and multiphysics simulation software | comsol |
| cuDNN | 7.5.0 | NVIDIA CUDA Deep Neural Network library | cudnn |
| DRAP | 1.91 | De novo RNA-seq Assembly Pipeline | DRAP |
| dvr-scan | 1.2.2 | Find and extract motion events in videos. | python |
| EMBOSS | 6.6 | Manipulating sequence files, among other things | seq_tools |
| EVidence Modeler | 1.1.1 | The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures | annotation |
| exonerate | 2.2.0 | Exonerate is a generic tool for pairwise sequence comparison | exonerate |
| fastp | 0.20.0 | A tool designed to provide fast all-in-one preprocessing for FastQ files. | qc, fastp |
| faSomeRecords | Retrieve fasta sequences from a multi-fasta file | seq_tools | |
| fasta-splitter.pl | 0.2.6 | Split FASTA files | seq_tools |
| FastQC | 0.11.7 | To assess the quality of DNA sequence data | qc |
| fastx-toolkit | 0.0.14 | To perform basic manipulations on DNA sequence data | qc |
| ffmpeg | 4.2.1 | AV conversion tools | ffmpeg |
| FLINT | 2.5.2 | Fast Library for Number Theory | flint |
| Funannotate | 2021-01.12 | Funannotate is a genome prediction, annotation, and comparison software package | funannotate |
| FUSTr | Families Under Selection in Transcriptomes | FUSTr | |
| Garli | 2.01 | Maximum likelihood phylogeny tree-search | phylogeny |
| GATK | 4.1.2.0 | Genome Analysis Toolkit | gatk |
| Gaussian | 16.B.01 | Computational chemistry | gaussian |
| gcc/g++/gfortran | 4.8.5 | Open source compiler collection | (none required) |
| 7.2.0 | Open source compiler collection (NOTE: Compiling with this version may cause conflicts with other software modules) | gcc | |
| GCTA | 1.92.3beta | Genome-wide Complex Trait Analysis | seq_tools |
| GMAP | 2019-06-10 | GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program | alignment |
| Gurobi Optimizer | 8.1.1 | 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 | 3.2 | Used for searching sequence databases for sequence homologs and for making sequence alignments | assembly_assessment |
| HTSeq | 0.11.2 | HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. | python/3.6 |
| HTStream | 1.0.0 | Quality control pipeline for High Throughput Sequencing data | qc |
| IBAMR | 0.7.1 | An adaptive and distributed-memory parallel implementation of the immersed boundary (IB) method | (not a module) |
| IDL | 8.7 | Programming language for data analysis and visualization | idl |
| ILOG CPLEX Studio | 12.9 | A mathematical optimization software package | CPLEX |
| ipyrad | 0.9.17 | Assembly and analysis of RAD-seq type genomic data sets | radseq |
| IQtree | 1.6.8 | Build phylogenetic trees from sequences | phylogeny |
| java | 12.0.2 | Java SE Development Kit | java |
| jellyfish | 2.2.10 | 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 |
| julia | 1.1.1 | A high-level general-purpose dynamic programming language designed for high-performance numerical analysis and computational science. | julia |
| kallisto | 0.46.1 | Map reads to a reference genome (without sketchiness) | alignment |
| Kraken2 | 2.1.1 | A taxonomic classification system | kraken2 |
| LAMMPS Molecular Dynamics Simulator | 2019.08.07 | LAMMPS is a classical molecular dynamics code with a focus on materials modeling. | lammps |
| MAFFT | 7 | Align sequences | alignment |
| magma | 2.24-8 | Magma is a software package designed for computations in algebra, number theory, algebraic geometry and algebraic combinatorics. | magma |
| Maker | 3..01.03 | MAKER is a portable and easily configurable genome annotation pipeline. | annotation |
| Mathematica | 12.3.1 | 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 | R2020a | Multi-paradigm numerical computing environment and programming language | matlab |
| Microsoft R Open | 3.5.1 | Enhanced distribution of R from Microsoft Corporation | ropen |
| mpich | 3.2.1 | Message Passing Interface project, generally used for running parallel code. | mpich |
| MrBayes | 3.2.7 | Building phylogenies | phylogeny |
| MultiQC | 1.9 | Aggregate results from bioinformatics analyses across many samples into a single report | python |
| ncbi-BLAST+ | 2.11.0+ | BLAST alignment to database. $NCBI_DATA set to top-level of weekly database downloads. | ncbi-blast |
| ngsTools | 2019-07-02 | methods for population genetics analyses from next-generation sequencing data | ngsTools |
| Oases | 0.2.08 | De novo transcriptome assembler for very short reads | assembly |
| Octave | 5.2.0 | Powerful mathematics-oriented syntax with built-in 2D/3D plotting and visualization tools | octave |
| OpenCV | 4.1.1 | Open source Computer Vision | opencv |
| openmpi | 1.10.7 | Message Passing Interface project, generally used for running parallel code. | openmpi |
| PAL2NAL | 14 | Force nucleotides onto protein alignments | alignment |
| PAML | 4.9h | Testing genes for selection | molecular_evolution |
| PARI/GP | 2.11.2 | PARI/GP is a widely used computer algebra system designed for fast computations in number theory | pari |
| PASA | 2.4.1 | PASA Pipeline | PASA |
| PCAngsd | 0.981 | Framework for analyzing low depth NGS data in heterogeneous populations using PCA | pcangsd |
| Perl | 5.30.1 | General purpose programming language | perl |
| prodigal | 2.6.3 | Prodigal Gene Prediction Software | assembly_assessment |
| pysam | 0.15.3 | Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. | python/3.6 |
| PySPH | 2020-08-19 | A framework for Smoothed Particle Hydrodynamics in Python | python/3.6 |
| Python | 3.6 | General purpose programming language (See modules list) | python |
| Python | 2.7 | General purpose programming language (See modules list) | python/2.7 |
| Qiime2 | 2019.7 | QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. | python/3.6 (source activate qiime2-2019.7) |
| R | 4.1.2 | Software environment for statistical computing and graphics | R |
| ROOT | 6.18.00 | Module scientific software toolkit for big data processing, statistical analysis, visualisation and storage. | ROOT |
| RSEM | 1.3.1 | Calculates read counts from BAM files | alignment |
| Sage | 9.4 | SageMath is a free open-source mathematics software system | sage |
| salmon | 1.4.0 | Map reads to a reference genome (wicked fast) | alignment |
| samtools | 1.11 | Manipulate sam and bam files | seq_tools |
| Scaff10X | 4.2 | Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads | assembly |
| seqtk | 1.3 | Toolkit for processing sequences in FASTA/Q formats | seq_tools |
| SIMULIA | 2019 | Software suite, including Abaqus and Tosca, for finite element analysis and computer-aided engineering | SIMULIA |
| singularity | 3.5.2 | Singularity is a container technology focused on building portable encapsulated environments. | singularity |
| SNeP | 1.1 | Historical Ne Trends | SNeP |
| SOAP de novo | r240 | Assembling genomes | assembly |
| SRA_Toolkit | 2.11.0 | Downloads files from the Sequence Read Archive | seq_tools |
| stacks | 2.41 | Population genetics with RAD data | stacks |
| STAR | 2.6.1 | Map reads to a reference genome | alignment |
| stringtie | 2.1.6 | Transcript assembly and quantification for RNA-Seq | assembly |
| Structure | 2.3.4 | software package for using multi-locus genotype data to investigate population structure. | structure |
| Tensorflow | 1.12.0 | Maching learning platform | python |
| TopHat | 2.1.1 | TopHat is a fast splice junction mapper for RNA-Seq reads. | alignment |
| TransDecoder | 5.5.0 | Identifies candidate coding regions within transcript sequences | transdecoder |
| TreeMix | 1.13 | Estimation of population trees with admixture | treemix |
| trimmomatic | 0.38 | To trim bad quality sequence data | qc |
| Trinity | 2.13.2 | For transcriptome assembly | assembly |
| Trinity (singularity) | 2.13.2 | For transcriptome assembly | Trinity |
| Trinnotate | 3.1.1 | For transcriptome assembly annotation | seq_annotation |
| vcftools | 0.1.16 | Manipulate vcf files | seq_tools |
| Velvet | 1.2.10 | Sequence assembler for very short reads | assembly |
| VEP | 97 | Variant Effect Predictor | seq_tools |
| XCrySDen | 1.6.2 | XCrySDen is a crystalline and molecular structure visualisation program | xcrysden |
| xmgrace | 5.1.25 | 2D plotting tool | xmgrace |