Software Item | Details | ||||||
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preseq | aimed at predicting and estimating the complexity of a genomic sequencing library
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prodigal | Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program.
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proj | PROJ is a generic coordinate transformation software that transforms geospatial coordinates from one coordinate reference system (CRS) to another.
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proj4 | Cartographic Projections Library
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provean | Protein Variation Effect Analyzer
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psycopg2 | a swiss-army knife of tools for a wide-range of genomics analysis tasks.
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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.
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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.
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pymvpa2 | PyMVPA stands for MultiVariate Pattern Analysis (MVPA) in Python.
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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.
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pyrad | Assembly and analysis of RADseq data sets
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python-anaconda-arc-connect | Python distribution for scientific computing, including accelerated commercial versions of several Python packages. Contains both Python 3 and Python2.
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python-anaconda2 | Python 2 distribution for scientific computing, including accelerated commercial versions of several Python packages.
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python-anaconda2-base | Python 2 distribution for scientific computing, including accelerated commercial versions of several Python packages.
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python-anaconda3 | Python 3 distribution for scientific computing, including accelerated commercial versions of several Python packages.
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python-anaconda3-base | Python 3 distribution for scientific computing, including accelerated commercial versions of several Python packages.
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python-antismash | Multipurpose programming language
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python-dev | Python is a general purpose programming language
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python-epd | Enthought Python Distribution
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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.
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QC3 | A quality control tool designed for DNA sequencing data
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qcli | Utilities for parsing command line options and arguments
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qiime | QIIME. (canonically pronounced chime) stands for Quantitative Insights Into Microbial Ecology.
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QoRTs | package for management of RNS-Seq datasets
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qpdf | QPDF is a command-line program that does structural, content-preserving transformations on PDF files.
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quast | QUAST evaluates genome assemblies.
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R | R environment for statistical computing and graphics
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r-biomed-libs | R libraries for bioinformatics, genomics, and sequencing.
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r8s | This package implements several methods to infer divergence times on a molecular
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raisd | RAiSD: Software for selective sweep detection.
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rate4site | Rate4Site is a program for detecting conserved amino-acid sites
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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.
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rclone | rclone is a command line program to sync files and directories to and from many cloud storage providers
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rdptools | The RDPTools project includes the modules from the RDP (Classifier, Clustering, SequenceMatch, ProbeMatch, InitialProcessing, FrameBot, ReadSeq, Xander) and all their dependencies.
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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).
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RepeatModeler | RepeatModeler is a de-novo repeat family identification and modeling package.
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RepeatTools | 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).
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reportlab | The ReportLab Toolkit. An Open Source Python library for generating PDFs and graphics.
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rfmix | RFMIX – Local Ancestry and Admixture Inference Version 2
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Rgeospatial | R environment for geospatial statistics
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Total pages: 13
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