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abaqus

Abaqus FEA product suite for engineering problems: vehicle loads, dynamic vibration, multibody systems, impact/crash, nonlinear static, thermal coupling, and acoustic-structural coupling.

Versions:6.14-1
License:Non-commercial research, Academic Institution License Agreement
Categories:FEA, dynamic vibration, impact/crash, thermal coupling
abinit

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis.

Versions:8.0.8 with gcc/5.4.0 openmpi/1.10.2
Categories:
aenet

Atomic Energy Network (aenet) is a software package [1] for the construction and usage of atomic interaction potentials based on artificial neural networks.

Versions:1.0.0
License:http://ann.atomistic.net/
Categories:atomic interaction potentials
allinea_forge

Parallel debugging and profiling tools, DDT and MAP.

Versions:6.0.6
License:Not available
Categories:Programming, debugger, performance, profiler
allinea_reports

Parallel profiling tool.

Versions:6.0.6
License:Not available
Categories:Programming, performance, profiler
amber

Amber refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

Versions:14
License:Campus Agreement
Categories:Computational Chemistry
ampl

AMPL algebraic modelling language.

Versions:20160714
License:http://ampl.com/buy-ampl-terms-and-conditions/
Categories:Optimization, algebraic modelling, linear programming
antlr

ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, processing, executing, or translating structured text or binary files.

Versions:2.7.7
License:Public Domain
Categories:Parser
anvio

Anvi’o is an analysis and visualization platform for ‘omics data.

Versions:2.0.2
License:GPL3
Categories:bioinformatics genomics analysis visualization gene
arc-admin-utils

ARC Admin Utilities

Versions:1.0
License:Admin
Categories:
armadillo

A high quality linear algebra library (matrix maths) for C++ language, aiming towards a good balance between speed and ease of use

Versions:7.200.2
License:http://arma.sourceforge.net/faq.html#licenses
Categories:C++, Programming, library
ase

Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.

Versions:3.11.0
License:https://wiki.fysik.dtu.dk/ase/development/licenseinfo.html
Categories:Atomic Simulation
ASTRID

ASTRID: Accurate Species TRees from Internode Distances. ASTRID is a ILS-aware tool for species tree estimation.

Versions:1.4
License:GNU GPL v3
Categories:bioinformatics
augustus

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.

Versions:3.2.2
License:GNU GPL
Categories:Eukaryotic genomic sequences, Genomic sequencing, gene prediction.
bamtools

BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files.

Versions:2.4.0
License:GPLv3
Categories:bioinformatics
bamUtil

Perform operations on SAM/BAM files

Versions:1.0.14
License:GPLv3
Categories:bioinformatics
bcftools

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF

Versions:1.3.1
License:GPLv2
Categories:bioinformatics
beagle

BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.

Versions:201606
License:GNU GPL v3 or GNU LGPL v3
Categories:bioinformatics, phylogenetics
beast2

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

Versions:2.4.2
License:GPLv2
Categories:bioinformatics
bedtools2

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

Versions:2.20.1; 2.25.0
License:GPLv2
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
blat

Standalone blat sequence search command line tool

Versions:34x1
License:GPLv2
Categories:bioinformatics
boost

Boost C++ library collection.

Versions:1.61.0; 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:2.2.9; 2.1.0
License:GPLv3
Categories:bioinformatics
bwa

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

Versions:0.7.15; 0.7.8; 0.5.9
License:GPLv3
Categories:bioinformatics
caffe

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

Versions: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:1.3
Categories:Sequencing, 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
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:1.0.2-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
chemkinpro

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

Versions:15151
License:combustion
Categories:
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
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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