Software Item | Details | ||||||
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beast2 | BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
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bedops | BEDOPS is an open-source command-linentoolkit that performs highly efficient and scalable Boolean and other setnoperations, statistical calculations, archiving, conversion and othernmanagement of genomic data of arbitrary scale.nTasks can be easily split by chromosome for distributing whole-genome analysesnacross a computational cluster.
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bedtools2 | a swiss-army knife of tools for a wide-range of genomics analysis tasks.
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berkeleygw | BerkeleyGW calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules.
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bigWigToBedGraph | The bigWigToBedGraph program converts from bigWig to bedGraph format.
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biom | The BIOM file format (canonically pronounced biome ) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project.
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bioperl | BioPerl is Perl tools for Bioinformatics, genomics and Life Sciences.
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biopython | The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
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blasr | Pacbio utilites for various sequence alignment tasks
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blast2 | Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool.
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blat | Standalone blat sequence search command line tool
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blender | Blender is a professional free and open-source 3D computer graphics software product used for creating animated films, visual effects, art, 3D printed models, interactive 3D applications and video games
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bless | Bloom-filter-based Error Correction Solution for High-throughput Sequencing Reads
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boost | Boost C++ library collection.
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boost-dev | Boost C++ library collection.
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bowtie | Bowtie is an ultrafast, memory-efficient short read aligner.
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bowtie2 | Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
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bpp-core | Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics.
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bpp-popgen | bpp-popgen: This library provides classes for population genetics analysis.
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bpp-seq | bpp-seq: This library provides classes to store and analyse biological sequences.
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bsclient | bsclient is a simple FTP-like command-line client for accessing and downloading data from an Illumina BASESPACE account.
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bucky | BUCKy is a free program to combine molecular data from multiple loci.
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busco | BUSCO v3 provides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB v9.
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bwa | BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
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cafe | Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
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caffe | Caffe is a deep learning framework made with expression, speed, and modularity in mind.
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canu | A single molecule sequence assembler for genomes large and small.
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cap3 | CAP3 is the third generation of the CAP sequence assembly program.
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cd-hit | CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses.
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cegma | CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome.
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cellprofiler | CellProfiler is free, open-source software for quantitative analysis of biological images.
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cellranger | Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.
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centrifuge | Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems.
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cfitsio | CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
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chemkin | Chemkin is for modeling and simulating complex gas phase and surface chemistry reactions that are used for the conceptual development of combustion systems.
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circlator | Circlator: a tool to circularize genome assemblies.
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circos | Circos description
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clang | The goal of the Clang project is to create a new C, C++, Objective C and Objective C++ front-end for the LLVM compiler.
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CLHEP | A Class Library for High Energy Physics
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clonalframeml | A software package that performs efficient inference of recombination in bacterial genomes. ClonalFrameML can be applied to any type of aligned sequence data, but is especially aimed at analysis of whole genome sequences.
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Total pages: 13
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