Search by title:
Software Item Details
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
License:Electronic Structure, Ab Initio, Density Functional Theory
Categories:
adapterremoval

This program searches for and removes remnant adapter sequences from your read data. The program can analyze both single end and paired end data. For detailed explanation of the parameters, please refer to the man page. For comments, suggestions and feedback please contact Stinus Lindgreen (stinus@binf.ku.dk) and Mikkel Schubert (MikkelSch@gmail.com).

Versions:2.1.7
License:GNU GENERAL PUBLIC LICENSE
Categories:bioinformatics
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
allele-seq

Allele Specific Expression and Binding in a Network Framework

Versions:1.2a
License:UNKNOWN
Categories:bioinformatics
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
almabte

This software is Open Source. almaBTE consists of a library and a collection of executables allowing the user to calculate thermal transport properties of heterogeneous structures, using only ab-initio data, and solving the phonon Boltzmann Transport Equation (BTE).

Versions:1.2
License:http://www.almabte.eu/
Categories:crystal structures, electronic structure, transport
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
annovar

ANNOVAR is a software tool to functionally annotate genetic variants detected from diverse genomes

Versions:2016Feb01
License:GPLv3
Categories:bioinformatics
ansys

ANSYS is a finite element simulation tool for multiphysics simulations.

Versions:17.1; 18.1
Categories:CFD, FEM, finite element, multiphysics
ansysem

ANSYS EM: HFSS and Maxwell

Versions:17.1; 18.1
Categories:CEM, EM, HFSS, maxwell
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
ANTsR

R with ANTsR available via site libraries.

Versions:2.1.0
License:ANTsR is Apache License 2.0 and R is GPL, https://www.r-project.org/Licenses/
Categories:ANTs, big data, data science, fMRI, graphics, image processing, image registration, statistics
anvio

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

Versions:2.2.2; 2.3.0; 2.1.0; 2.4.0; 2.3.2; 2.0.2
License:GPL3
Categories:Genomics, Visualization, bioinformatics
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
ataqv

A toolkit for measuring and comparing ATAC-seq results

Versions:0.9.5
License:unknown
Categories:bioinformatics
atomicrex

Atomicrex is a general purpose tool for the construction of atomic interaction models

Versions:0.1.6-25b340d
License:https://gitlab.com/atomicrex/atomicrex
Categories:atomic interaction
augustus

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

Versions:3.2.2; 3.2.2a
License:GNU GPL
Categories:Sequencing, bioinformatics, gene prediction.
bamql

BAMQL filters SAM or BAM files using a simple query language that is more expressive than the view options available in samtools.

Versions:1.4
License:UNKNOWN
Categories:bioinformatics
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
bayescan

BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial- Dirichlet model. One of the scenarios covered consists of an island model in which subpopulation allele frequencies are correlated through a common migrant gene pool from which they differ in varying degrees. The difference in allele frequency between this common gene pool and each subpopulation is measured by a subpopulation specific FST coefficient. Therefore, this formulation can consider realistic ecological scenarios where the effective size and the immigration rate may differ among subpopulations.

Versions:2.1
License:GNU GPL
Categories:Allele Frequencies, Migrant Gene Pool, bioinformatics
BayesTraits

BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available.

Versions:3
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; 2.4.5; 2.4.7
License:GPLv2
Categories:bioinformatics
bedops

BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable

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
blat

Standalone blat sequence search command line tool

Versions:34x1
License:GPLv2
Categories:bioinformatics
Current page: 1
Total pages: 10
Next