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gromacs

GROMACS performs Newtonian simulatons of molecular dynamics.

Versions:5.1.2 with gcc/4.9.3 openmpi/1.10.2; 5.1.2 with gcc/5.4.0 openmpi/1.10.2; 4.6.7 with gcc/5.4.0 openmpi/1.10.2
Categories:
gsl

GNU scientific libraries

Versions:1.16; 2.1
License:GPL
Categories:Programming, library, mathematics
gubbins

Genealogies Unbiased By recomBinations In Nucleotide Sequences

Versions:1.3.4
License:GPLv2
Categories:bioinformatics
gurobi

Gurobi optimization problem solver.

Versions:6.5.2
License:http://www.gurobi.com/pdfs/eula/eula-gurobi.pdf
Categories:Optimization, linear programming
hadoop

Configure Java for Hadoop

Versions:1.2
License:Not applicable
Categories:Utility
harminv

Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion – given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.

Versions:1.4
License:GPLv3
Categories:FDM, filter diagonalization method, harmonic inversion
hdf5

HDF5 data libraries and utilities.

Versions:1.8.16 with gcc/4.9.3; 1.8.16 with gcc/4.8.5; 1.8.16 with gcc/5.4.0; 1.8.16 with pgi/16.4; 1.8.16 with intel/16.0.3; 1.8.16 with intel/14.0.2
License:https://www.hdfgroup.org/products/licenses.html
Categories:Programming, Utility, library
hdf5-par

HDF5 data libraries and utilities.

Versions:1.8.16 with gcc/4.9.3; 1.8.16 with gcc/4.8.5; 1.8.16 with intel/16.0.3; 1.8.16 with intel/14.0.2
License:https://www.hdfgroup.org/products/licenses.html
Categories:Programming, Utility, library
helios

HELIOS Generalized Geometry Lattice Analysis package. Includes Casmo and Simulate from teh Studsvik suite.

Versions:1.12
License:?
Categories:Geometry Lattice Analysis, hexagonal VVER reactors, non-LWR lattices
hello

Hello world program for testing.

Versions:1.2
License:GPL
Categories:Utility, example
hisat2

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome).

Versions:2.0.4
License:http://www.gnu.org/licenses/gpl-3.0.html
Categories:Application, Biostatistics, python
hmmer

HMMER: biosequence analysis using profile hidden Markov models

Versions:3.1b2; 3.0
License:GNU GPL v3
Categories:Markov, Sequencing, bioinformatics
homer

HOMER is a suite of tools for Motif Discovery and ChIP-Seq analysis.

Versions:4.8
License:GPLv3
Categories:bioinformatics
HTSeq

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

Versions:2.20.1
License:GPLv2
Categories:bioinformatics
htslib

C library for high-throughput sequencing data formats

Versions:1.1
License:GPLv2
Categories:bioinformatics
idba

A Practical Iterative De Bruijn Graph De Novo Assembler related to Sequence assembly problem in bioinfomatics.

Versions:1.1.3
License:GPL2
Categories:bioinforatics sequencing
idl

IDL analysis and visualization software.

Versions:8.5
License:http://www.harrisgeospatial.com/company/legal/eula.aspx
Categories:Visualization
image-libraries

Image libraries

Versions:160610
License:more than one
Categories:Programming, gif, jpeg, libraries, png
impute

IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes. Most people use just a couple of the program’s basic functions, but we have also built up a collection of specialized and powerful options. If you are new to IMPUTE2, or indeed to phasing and imputation in general, we suggest that you start by learning the basics.

Versions:2.3.2
License:http://www.gnu.org/licenses/gpl.html
Categories:Application, Biostatistics, Math
indri

Indri is a search engine that provides state-of-the-art text search and a rich structured query language for text collections

Versions:5.9
License:GPLv2
Categories:bioinformatics
intel

Intel compiler suite.

Versions:14.0.2; 16.0.3
License:None provided
Categories:Core, Development, library
intel-tbb

IntelĀ® Threading Building Blocks (IntelĀ® TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable and composable, and that have future-proof scalability.

Versions:4.4-u5
License:GNU GPL v2
Categories:Programming, TBB, libraries
ipopt

Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale ?nonlinear optimization.

Versions:3.12.6
License:https://projects.coin-or.org/Ipopt
Categories:nonlinear optimization
ipyrad

ipyrad is a toolbox for assembly and analysis of RAD-seq type genomic data sets

Versions:0.4.1; 0.4.4
License:GPL3
Categories:bioinforatics assembly rad
jags

JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation

Versions:4.2.0
License:GNU GPL v2
Categories:Bayesian, MCMC, Markov
julia

Julia is a high-level, high-performance dynamic language for technical computing. The main homepage for Julia can be found at julialang.org.

Versions:0.4.6
License:MIT License
Categories:Programming
knitro

Knitro is an optimization software library for finding solutions of both continuous optimization models as well as discrete optimization models with integer or binary variables. Knitro is primarily designed for finding local optimal solutions of large sacle continuous nonlinear problems.

Versions:10.1.0-z
License:https://www.artelys.com/en/optimization-tools/knitro
Categories:Optimization, nonlinear solver
ksnp3

kSNP does SNP discovery and SNP annotation from whole genomes

Versions:3.021
License:GPLv2
Categories:bioinformatics
lahey

Lahey Fortran – f95/f90 fortran compiler

Versions:8.1b
Categories:Compiler, f95/f90, fortran
lammps

LAMMPS is a classical molecular dynamics code that models an ensemble of particles.

Versions:16Feb16; old-15May15
License:http://lammps.sandia.gov/doc/Section_intro.html#open-source-distribution
Categories:molecular dynamics
lapack

LAPACK is written in Fortran 90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.

Versions:3.4.2
License:http://www.netlib.org/lapack/LICENSE.txt
Categories:libraries
lenstool

A gravitational lensing software for modeling mass distribution of galaxies and clusters (strong and weak regime).

Versions:6.8.1
License:Unknown, contact author jean-paul.kneib@lam.fr
Categories:Gravitation, cluster mass distribution modeling., galaxy mass distribution modeling, gravitational lensing
libctl

Guile-based library implementing flexible control files for scientific simulations.

Versions:3.2.2
License:GPL
Categories:Utility, library
liftOver

liftOver converts genome coordinates between assemblies

Versions:1.0.0
License:GPLv3
Categories:bioinformatics
ls-bsr

Large Scale Blast Score Ratio

Versions:1.0
License:GPLv3
Categories:bioinformatics
mach

MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

Versions:1.0.18
License:Math, Biostatistics, Application
Categories:
macs2

Model-based Analysis of ChIP-Seq (MACS), for identifying transcript factor binding sites.

Versions:2.1.0
License:GPLv2
Categories:bioinformatics
mafft

MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc.

Versions:7.294
License:http://mafft.cbrc.jp/alignment/software/license66.txt
Categories:Alignment, bioinformatics
mageck

Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout

Versions:0.5.2
License:GPLv3
Categories:bioinformatics
maker

MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.

Versions:2.3.8
License:Perl Foundation Artistic License 2.0 and GNU GPL
Categories:Genome annotation, ab-initio gene prediction, trainable gene prediction
Current page: 3
Total pages: 7
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