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cmake

CMake cross-platform make system.

Versions:3.5.2
License:https://cmake.org/licensing/
Categories:Compiler, Programming, Utility
converge

CONVERGE is a CFD code with adaptive meshing.

Versions:2.3.13_180716; 2.2.0_082115
License:Provided by licensed labs
Categories:CFD, Fluid dynamics, adaptive mesh
crt

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats.

Versions:1.2
License:GPLv3
Categories:bioinformatics
cubit

CUBIT is a full-featured software toolkit for robust generation of two- and three-dimensional finite element meshes.

Versions:13.2
License:https://cubit.sandia.gov/public/licensing.html
Categories:mesh
cuda

CUDA compilers and libraries.

Versions:7.5; 6.5; 8.0.44; 8.0.27rc
License:http://docs.nvidia.com/cuda/eula/index.html
Categories:CUDA, Programming, gpu, library
cudnn

cuDNN libraries.

Versions:7.0-v4; 6.5-v2; 7.5-v5
License:http://docs.nvidia.com/cuda/eula
Categories:CUDA, Programming, cuDNN, deep learning, gpu, library, neural network
cufflinks

Transcriptome assembly and differential expression analysis for RNA-Seq.

Versions:2.2.0; 2.1.1
License:Cufflinks is provided under the OSI-approved Boost License
Categories:bioinformatics
cutadapt

cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.

Versions:1.10
License:Public Domain
Categories:Sequencing, bioinformatics
cython

The Cython compiler for writing C extensions for the Python language

Versions:0.16
License:GPLv3
Categories:bioinformatics
dendropy

Dendropy is a Python library for phylogenetic computing.

Versions:3.12.0
License:Copyright 2009-2016, Jeet Sukumaran and Mark T. Holder. All rights reserved.
Categories:bioinformatics
dmtcp

DMTCP is a tool to transparently checkpoint the state of multiple simultaneous applications, including multi-threaded and distributed applications.

Versions:3.0.0
License:https://github.com/dmtcp/dmtcp/blob/master/COPYING
Categories:Programming, Utilities
elsa

ELSA: Extended Local Similarity Analysis

Versions:1.0.2
License:GPLv3
Categories:bioinformatics
emirge

EMIRGE reconstructs full length ribosomal genes from short read sequencing data.

Versions:0.60.3
License:GNU GPL v3
Categories:Reconstruction, Sequencing, bioinformatics
espresso

Quantum ESPRESSO is an integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale.

Versions:5.4.0; old-5.1.1
License:http://www2.mmm.ucar.edu/wrf/users/public.html
Categories:ab initio quantum chemistry, electronic structure, materials modeling
exonerate

Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.

Versions:2.2.0
License:GPLv3
Categories:automated generation of heuristics., biological sequence comparison, pairwise sequence comparison, sequence alignment
fastml

Used for the reconstruction of ancestral sequences. gub version adds functionality for gubbins software

Versions:gub; 3.1
License:GPLv2
Categories:bioinformatics
fastqc

A quality control tool for high throughput sequence data.

Versions:0.10.1
License:GPLv3
Categories:bioinformatics
fastStructure

fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.

Versions:1.0
License:MIT License
Categories:Genotype, bioinformatics
fasttree

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.

Versions:2.1.9
License:GPLv3
Categories:bioinformatics
fdtd-solutions

Lumerical FDTD Solutions is a high performance 3D FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials.

Versions:8.16.903
License:commercial, https://www.lumerical.com/tcad-products/licensing/license_agreement.html
Categories:3D, FDTD, Optimization, analysis, design, maxwell, optics, photonics, solver
ffmpeg

FFMPEG is a complete, cross-platform solution to record, convert and stream audio and video.

Versions:3.0.2
License:https://ffmpeg.org/legal.html
Categories:audio, codec, transcoder, video
fftw

Libraries for computation of discrete Fourier transform.

Versions:3.3.4 with gcc/4.9.3; 3.3.4 with gcc/4.8.5; 3.3.4 with gcc/5.4.0; 3.3.4 with intel/16.0.3; 3.3.4 with intel/14.0.2; 2.1.5 with gcc/4.8.5; 2.1.5 with intel/16.0.3
License:http://www.fftw.org/fftw3_doc/License-and-Copyright.html
Categories:Core, Development, library
flexbar

The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences.

Versions:2.7.0
Categories:Sequencing, bioinformatics
flexlm

FLEXlm utility programs.

Versions:11.11.1.2
License:None provided
Categories:Utility
flux-utils

flux-utils is a collection of utilities for the FLux and Armis HPC clusters.

Versions:1.0
License:GPL-3
Categories:Armis, Flux, Utilities
freebayes

Bayesian genetic variant detector designed to find small polymorphisms

Versions:1.0.2.33
License:MIT software license
Categories:bioinformatics genetics bayesian detector polymorphisms
freesurfer

FreeSurfer MRI processing and analysis software.

Versions:5.3.0
License:http://freesurfer.net/fswiki/FreeSurferSoftwareLicense
Categories:MRI, neuroimaging, neuroscience
fsl

FSL suite of MRI neuroimaging tools.

Versions:5.0.9
License:http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
Categories:DTI, fMRI, neuroimaging, neuroscience
g95

G95 – f95/f90 fortran compiler

Versions:0.94
License:fortran, compiler
Categories:
gatk

The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it’s a suite of tools for working with the human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and local realigner.

Versions:3.5; 3.6; 3.2-2
License:Broad Institute Software License Agreement
Categories:bioinformatics
gaussian

Gaussian is an electronic structure program that predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types.

Versions:09-revD01
Categories:electronic structure, molecular
gcc

GNU compiler suite

Versions:4.8.5; 4.9.3; 5.4.0
License:GPL
Categories:Compiler, Development, Programming
gdal

GDAL is a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation.

Versions:2.1.0
License:MIT (http://svn.osgeo.org/gdal/trunk/gdal/LICENSE.TXT)
Categories:GIS, Geospatial, OGR
geneid

geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure.

Versions:1.4.4
License:GNU GPL v2
Categories:bioinformatics
genometools

The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt.

Versions:1.5.9
License:GPLv3
Categories:bioinformatics
geos

GEOS (Geometry Engine – Open Source) is a C++ port of the Java Topology Suite (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced topology functions.

Versions:3.5.0
License:GNU LGPL v2.1
Categories:GIS, Geometry, OSGeo
gffcompare

The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the ‘query’ files), when compared with a reference annotation (also provided as GFF).

Versions:0.9.7
License:https://opensource.org/licenses/Artistic-2.0
Categories:Application, Math, bioinformatics
ghostscript

Ghostscript is an interpreter for the PostScript language and for PDF.

Versions:9.19
License:GPLv3
Categories:bioinformatics
go

Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.

Versions:1.6.2
License:https://golang.org/LICENSE?m=text
Categories:Go, Programming
gotcloud

GotCloud contains Mapping & Variant Calling Pipelines.

Versions:master
License:GPLv3
Categories:
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Total pages: 7
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