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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:
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; 201704
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:201607; latest; 201704
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:201607; latest; latest-3.6; 201704
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

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] Q-Chem is a comprehensive ab initio quantum chemistry package for accurate predictions of molecular structures, reactivities, and vibrational, electronic and NMR spectra.

Versions:experimental with 4.4/intel; 3.2; 4.4 with OpenMPI/intel; 4.4 with serial/intel
License:See https://www.q-chem.com/qchem-website/about-qchem4.html for how to obtain a 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:
qiime

QIIME. (canonically pronounced chime) stands for Quantitative Insights Into Microbial Ecology.

Versions:2.0.6
License:GPLv2
Categories:bioinformatics
quast

QUAST evaluates genome assemblies.

Versions:4.3
License:GPL2
Categories:bioinformatics assemblies
R

R environment for statistical computing and graphics

Versions:3.3.0; 3.3.2; 3.3.3
License:GPL, https://www.r-project.org/Licenses/
Categories:big data, data science, graphics, statistics
r-biomed-libs

R libraries for bioinformatics, genomics, and sequencing.

Versions:3.3; 3.3.2
License:GPLv2
Categories:bioinformatics
raxml

RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for post-analyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads.

Versions:8.2.8; 7.2.8
License:GNU GPL v3
Categories:Phylogentics, bioinformatics
rdptools

The RDPTools project includes the modules from the RDP (Classifier, Clustering, SequenceMatch, ProbeMatch, InitialProcessing, FrameBot, ReadSeq, Xander) and all their dependencies.

Versions:1.0.0
License:https://github.com/rdpstaff/RDPTools
Categories:Application, Biostatistics, Java
repeatmasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).

Versions:4.0.6
License:OSL-2.1
Categories:DNA sequence, DNA sequence masking., DNA sequence scanning
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Total pages: 9
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