![]() ![]() SageMath is a free open-source mathematics software system 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. Software environment for statistical computing and graphics General purpose programming language ( See modules list) Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files.Ī framework for Smoothed Particle Hydrodynamics in Python PLINK is a free, open-source whole genome association analysis toolset PARI/GP is a widely used computer algebra system designed for fast computations in number theory Message Passing Interface project, generally used for running parallel code.įorce nucleotides onto protein alignments Powerful mathematics-oriented syntax with built-in 2D/3D plotting and visualization tools $NCBI_DATA set to top-level of weekly database downloads.ĭe novo transcriptome assembler for very short reads Sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomicsĪggregate results from bioinformatics analyses across many samples into a single reportīLAST alignment to database. Multi-paradigm numerical computing environment and programming language MAKER is a portable and easily configurable genome annotation pipeline.Ī modern technical computing system spanning most areas of technical computing - including neural networks, machine learning, image processing, geometry, data science, visualizations, and others. Magma is a software package designed for computations in algebra, number theory, algebraic geometry and algebraic combinatorics. LAMMPS is a classical molecular dynamics code with a focus on materials modeling. Map reads to a reference genome (without sketchiness) Tool for fast, memory-efficient counting of k-mers in DNAįind the best model of sequence evolution for building phylogenies Quality control pipeline for High Throughput Sequencing dataĪn adaptive and distributed-memory parallel implementation of the immersed boundary (IB) methodĪ mathematical optimization software packageĪssembly and analysis of RAD-seq type genomic data sets ![]() Used for searching sequence databases for sequence homologs and for making sequence alignments Graph-based alignment of next generation sequencing reads to a population of genomes GSNAP: Genomic Short-read Nucleotide Alignment ProgramĪn 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) GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and To perform basic manipulations on DNA sequence dataįunannotate is a genome prediction, annotation, and comparison software package To assess the quality of DNA sequence data Retrieve fasta sequences from a multi-fasta file The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structuresĮxonerate is a generic tool for pairwise sequence comparisonĪ tool designed to provide fast all-in-one preprocessing for FastQ files. Manipulating sequence files, among other things The NVIDIA CUDA® Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.įind and extract motion events in videos. The NVIDIA® CUDA® Toolkit provides a development environment for creating high performance GPU-accelerated applications. ![]() Utility script to construct species phylogenies using BUSCOsĪ single molecule sequence assembler for genomes large and small.Ī finite element analysis, solver and multiphysics simulation software Perl tools for bioinformatics, genomics, and life scienceīayesian Reestimation of Abundance with KrakENīRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes Predicts genes in eukaryotic genomic sequencesīBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence dataīCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCFīEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. If you need additional software, please submit a request by emailing some software packages have specific instructions that are necessary to follow. Most software packages are added and removed from your environment using Environment Modules (e.g. From top level menus, use escape to exit the menu.īelow is a list of software available on BisonNet. Within a submenu, use escape to move to top level menu parent. Use up and down arrow keys to explore within a submenu. Use left and right arrow keys to navigate between menus.
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