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oclust

Pipeline for clustering long 16S rRNA sequencing reads, or any sequences, into Operational Taxonomic Units.

Versions:1.0.0
License:GPLv2
Categories:bioinformatics
openblas

BLAS provides standard interfaces for linear algebra, including BLAS1 (vector-vector operations), BLAS2 (matrix-vector operations), and BLAS3 (matrix-matrix operations).

Versions:0.2.18
License:https://opensource.org/licenses/BSD-3-Clause
Categories:C++, Programming, library
opencv

OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.

Versions:2.4.13
License:http://opencv.org/
Categories:computer vision, machine learning
openfoam

OpenFOAM is a free, open source CFD software.

Versions:3.0+dev20160616; 3.0+; 2.4.0; old-1.6-ext-07122012
License:http://www.openfoam.com/documentation/licencing.php
Categories:CFD
openmpi

OpenMPI implementation of the MPI protocol

Versions:1.10.2 with gcc/4.8.5; 1.10.2 with gcc/4.9.3; 1.10.2 with gcc/5.4.0; 1.10.2 with intel/16.0.3; 1.10.2 with intel/14.0.2; 1.10.2 with pgi/16.4; 1.6.5 with gcc/4.8.5; 1.6.5 with intel/14.0.2; 1.8.8 with intel/14.0.2
License:https://www.open-mpi.org/community/license.php
Categories:Core, Development, Utility
orange

Orange is a component-based data mining software. It includes a range of data visualization, exploration, preprocessing and modeling techniques.

Versions:3.0
License:http://orange.biolab.si/license/
Categories:Programming, library, python
p7zip

p7zip is a port of 7za.exe, compression app, for POSIX systems like Unix.

Versions:15.14.1
License:http://www.7-zip.org/license.txt
Categories:7zip, archiver, archives, compression, zip
parallel

GNU parallel is a shell tool for executing jobs in parallel using one or more computers.

Versions:20161022
License:GPLv3
Categories:bioinformatics
paraview

Paraview data analysis and visualization application.

Versions:5.1.0
License:http://www.paraview.org/paraview-license/
Categories:Visualization, data analysis
parmetis

ParMETIS – Parallel Graph Partitioning and Fill-reducing Matrix Ordering

Versions:4.0.3-intel-16.0.3
License:http://glaros.dtc.umn.edu/gkhome/metis/parmetis/download
Categories:matrices, matrix, ordering, partitioning
pbh5tools

A swiss-army knife for interrogating PacBio HDF5 files (cmp.h5, bas.h5)

Versions:1.0
License:Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
Categories:bioinformatics
pdl

PDL turns Perl into a free, array-oriented, numerical language similar to IDL and MatLab.

Versions:2.016
License:The Perl 5 License (Artistic 1 & GPL 1)
Categories:Perl, arrays, data, numerical, scientific
perl-modules

Perl addin modules for use with Perl version 5.16.3.

Versions:1.0
License:GPLv2
Categories:bioinformatics
perlmods

Various CPAN modules

Versions:5.16.3
License:Perl Artistic License
Categories:
pgi

Compiler suite.

Versions:16.4
License:http://www.pgroup.com/doc/LICENSE.txt
Categories:Compiler, Development, debugger, profiler
pgplot

The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time.

Versions:5.2.2
License:PGPLOT, Graphics Subroutine Library
Categories:
phyloassigner

PhyloAssigner is a Perl pipeline for phylogenetic classification of amplicon pyrosequences.

Versions:6.166
License:GPL3
Categories:bioinformatics
phylosift

PhyloSift is a suite of software tools to conduct phylogenetic analysis of genomes and metagenomes.

Versions:1.0.1
License:GPL3
Categories:bioinformatics
phyml

PhyML is a software package which primary task that is to estimate maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences.

Versions:3.2.20160530
License:GPL3
Categories:bioinformatives phylogeny
picard

A set of tools for working with high-throughput sequencing data

Versions:1.79; 1.76
License:MIT License, Apache License V2.0
Categories:bioinformatics
piler-cr

PILERCR is public domain software for finding CRISPR repeats.

Versions:1.06
License:GPLv3
Categories:bioinformatics
plink

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

Versions:1.9
License:GPLv3
Categories:bioinformatics
popoolation2

PoPoolation2 allows comparision of allele frequencies for SNPs between two or more populations and identification of significant differences.

Versions:1.201
License:Unknown
Categories:bioinformatics
povray

High-quality raytracer for 3D graphics.

Versions:3.7
Categories:
pplacer

Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.

Versions:1.1.alpha18
License:GPL3
Categories:bioinformatics
prank

PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences.

Versions:150803
License:GPLv3
Categories:bioinformatics
prodigal

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program.

Versions:2.6.3; 2.6.2
License:GPL3
Categories:Bioinformatics gene genefinding genetics
proj4

Cartographic Projections Library

Versions:4.9.2
License:MIT
Categories:GIS, library
psycopg2

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

Versions:2.6.1
License:GPLv2
Categories:bioinformatics
pycogent

PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics.

Versions:1.9
License:GPLv2
Categories:
pyqi

pyqi (canonically pronounced pie chee) is a Python framework designed to support wrapping general commands in multiple types of interfaces, including at the command line, HTML, and API levels.

Versions:0.3.2
License:BSD
Categories:
pyrad

Assembly and analysis of RADseq data sets

Versions:3.0.66; 3.0.5
License:GNU GPL v3
Categories:Assembly, bioinformatics
python-anaconda-arc-connect

Python distribution for scientific computing, including accelerated commercial versions of several Python packages. Contains both Python 3 and Python2.

Versions:latest
License:Academic Cluster License, https://docs.continuum.io/anaconda/eula
Categories:IPython, Jupyter, Programming, astropy, biopython, matplotlib, numpy, python, scipy, scripting
python-anaconda2

Python 2 distribution for scientific computing, including accelerated commercial versions of several Python packages.

Versions:latest; 201607
License:Academic Cluster License, https://docs.continuum.io/anaconda/eula
Categories:IPython, Jupyter, Programming, astropy, biopython, matplotlib, numpy, python, scipy, scripting
python-anaconda3

Python 3 distribution for scientific computing, including accelerated commercial versions of several Python packages.

Versions:latest; 201607
License:Academic Cluster License, https://docs.continuum.io/anaconda/eula
Categories:IPython, Jupyter, Programming, astropy, biopython, matplotlib, numpy, python, scipy, scripting
python-dev

Python is a general purpose programming language

Versions:3.5.2
License:https://opensource.org/licenses/Python-2.0
Categories:Programming, language
python-epd

Enthought Python Distribution

Versions:7.6-1
License:GPL
Categories:Programming, library, matplotlib, numpy, python, scipy
Q-chem

Q-Chem is a comprehensive ab initio quantum chemistry package for accurate predictions of molecular structures, reactivities, and vibrational, electronic and NMR spectra.

Versions:3.2; 4.4 with intel/16.0.3; experimental with 4.4/intel
License:Requires Q-chem developer license.
Categories:DFT, Hartree-Fock, Molecular structure, Quantum Chemistry, vibrational spectroscopy.
QC3

A quality control tool designed for DNA sequencing data

Versions:1.33
License:GPLv2
Categories:bioinformatics
qcli

Utilities for parsing command line options and arguments

Versions:0.1.1
License:GPL
Categories:
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