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beast2

BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.

Versions:2.4.2; 2.4.5; 2.4.7
License:GPLv2
Categories:bioinformatics
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.

Versions:2.4.26
License:GNU GPL v2
Categories:Genomics, bioinformatics
bedtools2

a swiss-army knife of tools for a wide-range of genomics analysis tasks.

Versions:2.25.0; 2.20.1
License:GPLv2
Categories:bioinformatics
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.

Versions:1.2.0
License:http://www.berkeleygw.org/?q=node/6
Categories:materials, quasiparticle properties
bigWigToBedGraph

The bigWigToBedGraph program converts from bigWig to bedGraph format.

Versions:3.0.2
License:GPLv3
Categories:bioinformatics
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.

Versions:2.1.5-dev
Categories:
bioperl

BioPerl is Perl tools for Bioinformatics, genomics and Life Sciences.

Versions:1.6.1; 1.6.924
License:GPLv3
Categories:bioinformatics
biopython

The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.

Versions:1.60
License:GPLv2
Categories:bioinformatics
blasr

Pacbio utilites for various sequence alignment tasks

Versions:5.1
License:GPLv2
Categories:bioinformatics
blast2

Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool.

Versions:2.2.26
License:United States Government Work under the terms of the United States Copyright Act
Categories:bioinformatics
blat

Standalone blat sequence search command line tool

Versions:34x1
License:GPLv2
Categories:bioinformatics
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

Versions:2.78c
License:https://www.blender.org/about/license
Categories:3D modeling, simulation, vizualization
bless

Bloom-filter-based Error Correction Solution for High-throughput Sequencing Reads

Versions:1.02
License:GPL v3
Categories:bioinformatics sequencing
boost

Boost C++ library collection.

Versions:1.54.0; 1.69.0; 1.61.0; 1.64.0; 1.57.0
License:http://www.boost.org/users/license.html
Categories:C++, Programming, library
boost-dev

Boost C++ library collection.

Versions:1.61.0
License:http://www.boost.org/users/license.html
Categories:C++, Programming, library
bowtie

Bowtie is an ultrafast, memory-efficient short read aligner.

Versions:1.0.0
License:GPLv3
Categories:bioinformatics
bowtie2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

Versions:2.3.4.3; 2.1.0; 2.3.3; 2.3.2; 2.3.1; 2.2.9
License:GPLv3
Categories:bioinformatics
bpp-core

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics.

Versions:2.4.0
License:CeCILL 3
Categories:bioinformatics
bpp-popgen

bpp-popgen: This library provides classes for population genetics analysis.

Versions:2.4.0
License:CeCILL 3
Categories:bioinformatics
bpp-seq

bpp-seq: This library provides classes to store and analyse biological sequences.

Versions:2.4.0
License:CeCILL 3
Categories:bioinformatics
bsclient

bsclient is a simple FTP-like command-line client for accessing and downloading data from an Illumina BASESPACE account.

Versions:0.4.1a
License:GPLv3
Categories:bioinformatics
bucky

BUCKy is a free program to combine molecular data from multiple loci.

Versions:1.4.4
License:GPL v2
Categories:BCA, Bayesian, Concordance
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.

Versions:3.0.2
License:MIT License
Categories:bioinformatics
bwa

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.

Versions:0.7.3a; 0.5.9; 0.7.8; 0.7.15
License:GPLv3
Categories:bioinformatics
cafe

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

Versions:4.1
License:https://github.com/hahnlab/CAFE/blob/master/LICENSE
Categories:bioinformatics
caffe

Caffe is a deep learning framework made with expression, speed, and modularity in mind.

Versions:170407; 160803
License:https://github.com/BVLC/caffe/blob/master/LICENSE
Categories:deep learning, machine learning
canu

A single molecule sequence assembler for genomes large and small.

Versions:1.8; 1.3
Categories:Sequencing, bioinformatics
cap3

CAP3 is the third generation of the CAP sequence assembly program.

Versions:2015-02-10
License:GPLv3
Categories:bioinformatics
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.

Versions:4.6.4; 2016-0711
Categories:
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.

Versions:2.5
License:GNU GPL v2
Categories:bioinformatics
cellprofiler

CellProfiler is free, open-source software for quantitative analysis of biological images.

Versions:3.0.0rc1-20170814; 3.1.8
License:BSD 3-clause license
Categories:analysis, bioinformatics, biology, imaging
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.

Versions:2.1.1
Categories:Alignment, RNA, bioinformatics
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.

Versions:1.0.3-beta; 1.0.2-beta
License:GPL3
Categories:bioinformatices sequencing indexing gene classifications reads genome
cfitsio

CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.

Versions:3.390
License:Public Domain
Categories:Astronomy, FITS, Image
chemkin

Chemkin is for modeling and simulating complex gas phase and surface chemistry reactions that are used for the conceptual development of combustion systems.

Versions:17.1; 18.1
Categories:combustion
circlator

Circlator: a tool to circularize genome assemblies.

Versions:1.5.5
License:GPLv3
Categories:bioinformatics
circos

Circos description

Versions:0.69-3
License:GPLv3
Categories:bioinformatics
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.

Versions:3.8.1
License:University of Illinois/NCSA Open Source License
Categories:Compiler, LLVM
CLHEP

A Class Library for High Energy Physics

Versions:2.4.0.2
License:GPL
Categories:Research Development
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.

Versions:1.0-19
License:GNU GPL v3 https://www.gnu.org/copyleft/gpl.html
Categories:Biostatistics, Software
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Total pages: 13
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