Search by title:
Software Item Details
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; 3.1.0; 3.2.0
License:http://opencv.org/
Categories:computer vision, machine learning
opencv-python

This module sets up PYTHONPATH for python-anaconda to use OpenCV.

Versions:2; 3
License:N/A
Categories:python
openfoam

OpenFOAM is a free, open source CFD software.

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

OpenMPI implementation of the MPI protocol

Versions:1.8.8 with gcc/4.8.5; 1.8.8 with intel/14.0.2; 1.6.5 with gcc/4.8.5; 1.6.5 with intel/14.0.2; 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/14.0.2; 1.10.2 with intel/16.0.3; 1.10.2 with intel/17.0.1; 1.10.2 with pgi/16.4; 1.8.3 with intel/16.0.3
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
p4vasp

This software is Open Source. p4VASP is a visualization suite for the Vienna Ab-initio Simulation Package (VASP).

Versions:0.3.29
License:http://www.p4vasp.at
Categories:crystal symmetries, electronic structure, vizualization
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
paml

PAML (for Phylogenetic Analysis by Maximum Likelihood) is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood.

Versions:4.9d
License:UNKNOWN
Categories:bioinformatics
parallel

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

Versions:20161022
License:GPLv3
Categories:bioinformatics
paraver

Expressive powerful and flexible trace visualizer for post-mortem trace analysis.

Versions:4.6.4
License:LGPLv2.1
Categories:Trace Analysis, Visualiztion, performance
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; 4.0.3-intel-17.0.1
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
pear

PEAR – Paired-End reAd mergeR

Versions:0.9.6
License:GPLv2
Categories:bioinformatics
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:
petsc

PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.

Versions:3.7.4
License:http://www.mcs.anl.gov/petsc/documentation/license.html
Categories:data structures, partial differential equations, scientific routines
PGDSpider

An automated data conversion tool for connecting population genetics and genomics programs

Versions:2.1.1.0
License:BSD 3-Clause License, see LICENSE.txt
Categories:Conversion, Genomics, bioinformatics, genetics
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:
phrap_cross_match

cross_match is a general purpose utility for comparing any two DNA sequence sets using a ‘banded’ version of swat.

Versions:1.0
License:UNKNOWN
Categories:bioinformatics
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:2.4.1; 1.76; 2.3.0; 1.79
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:2.6.2; 2.6.3
License:GPL3
Categories:Bioinformatics gene genefinding genetics
proj4

Cartographic Projections Library

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

Protein Variation Effect Analyzer

Versions:1.1.5
License:GPLv2
Categories:bioinformatics
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:
pyinstaller

PyInstaller bundles a Python application and all its dependencies into a single package. The user can run the packaged app without installing a Python interpreter or any modules.

Versions:3.2
License:Python, Application, Utility
Categories:
Current page: 7
Total pages: 10
Previous
Next