Pybedtools 0.8.0 – Python extension to BEDTools

Pybedtools 0.8.0

:: DESCRIPTION

Pybedtools is a Python wrapper for Aaron Quinlan’s BEDtools and extends these “genome algebra” programs by offering feature-level manipulations from with Python.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX
Python

:: DOWNLOAD

Pybedtools

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Dec 15;27(24):3423-4. doi: 10.1093/bioinformatics/btr539
Pybedtools: a flexible Python library for manipulating genomic datasets and annotations.
Dale RK, Pedersen BS, Quinlan AR.

scikit-bio 0.5.5 – Python 3 package providing Data Structures, Algorithms and Educational Resources for Bioinformatics

scikit-bio 0.5.5

:: DESCRIPTION

scikit-bio is an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows /MacOsX
Python

:: DOWNLOAD

scikit-bio

:: MORE INFORMATION

ETE 3.1.1 – Python Environment for Phylogenetic Tree Exploration

ETE 3.1.1

:: DESCRIPTION

ETE (Environment for Tree Exploration ) is a python programming toolkit that assists in the automated manipulation, analysis and visualization of phylogenetic and other type of trees. It provides a wide range of tree handling methods, node annotation features, programmatic access to the phylomeDB database, and automatic orthology and paralogy prediction methods. In addition, an interactive tree visualization program, as well as a highly customizable tree drawing engine, is included.

::DEVELOPER

Gabaldón’s lab

:: SCREENSHOTS

N/A

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Mac OsX / Linux
Python

:: DOWNLOAD

ETE

:: MORE INFORMATION

Citation:

ETE 3: Reconstruction, analysis and visualization of phylogenomic data.
Huerta-Cepas J, Serra F, Bork P.
Mol Biol Evol. 2016 Feb 26. pii: msw046.

Jaime Huerta-Cepas*, Joaquín Dopazo and Toni Gabaldón*.
ETE: a python Environment for Tree Exploration.
BMC Bioinformatics 2010, 11:24.

pychem 3.05g – Python and Chemometrics package

pychem 3.05g

:: DESCRIPTION

PyChem (Python and Chemometrics) is a package for univariate and multivariate data analysis.

::DEVELOPER

Roger Jarvis (Roger.Jarvis@manchester.ac.uk )

:: SCREENSHOTS

:: REQUIREMENTS

Linux / MacOsX / Window
Python

:: DOWNLOAD

pychem

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Oct 15;22(20):2565-6. Epub 2006 Jul 31.
PYCHEM: a multivariate analysis package for python.
Jarvis RM, Broadhurst D, Johnson H, O’Boyle NM, Goodacre R.

Pygr 0.82 – Python Graph Database Framework for Bioinformatics

Pygr 0.82

:: DESCRIPTION

pygr is a bioinformatics toolkit for sequence analysis and comparative genomics. pygr is highly scalable (e.g. one can easily query multi-genome alignments) and easy to use

Pygr is open source software to develop graph database interfaces for the popular Python language to make it easy to do powerful sequence and comparative genomics analyses, even with extremely large multi-genome data sets. pygr includes:

Code for interacting with sequence databases, search methods such as BLAST, repeat-masking, megablast, etc.;
Querying and working with sequence annotation databases and sequence alignment datasets;
A data namespace for accessing a given resource with seamless data relationship management.
Easy data sharing that includes transparent access over network protocols.
High performance graph representation and query of interval-based data.

::DEVELOPER

Chris Lee, Dept. of Chemistry & Biochemistry,UCLA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/Mac OsX
Python

:: DOWNLOAD

Pygr

:: MORE INFORMATION

PyPLIF 0.1.1 – Python-based Protein-Ligand Interaction Fingerprinting

pyplif 0.1.1

:: DESCRIPTION

PyPLIF is a program/script written in Python to analyze protein-ligand interaction from the molecular docking result.

::DEVELOPER

Muhammad Radifar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOsX / Linux
Python

:: DOWNLOAD

pyplif

:: MORE INFORMATION

Citation:

Bioinformation. 2013;9(6):325-8. doi: 10.6026/97320630009325. Epub 2013 Mar 19.
PyPLIF: Python-based Protein-Ligand Interaction Fingerprinting.
Radifar M, Yuniarti N, Istyastono EP.

protpy 1.0 – Development of Protein Descriptors using Python

protpy 1.0

:: DESCRIPTION

protpy (protein in python)is a software for calculating the widely used structural and physicochemical features of proteins and peptides from amino acid sequence.

::DEVELOPER

Research Center of Modernization of Traditional Chinese Medicines, Central South University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux / Mac OsX
Python

:: DOWNLOAD

protpy

:: MORE INFORMATION

Citation

Bioinformatics (2013) 29 (7): 960-962.
propy: a tool to generate various modes of Chou’s PseAAC.
Cao DS, Xu QS, Liang YZ.

fRNAkenstein 20130115 – Python program for Multiple Target Inverse RNA Folding

fRNAkenstein 20130115

:: DESCRIPTION

Frnakenstein is a python program for solving the inverse RNA folding problem, i.e. given a target structure it attempts to design a sequence folding into this stucture.

:: DEVELOPER

James W. J. Anderson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
Python

:: DOWNLOAD

fRNAkenstein

:: MORE INFORMATION

BMC Bioinformatics. 2012 Oct 9;13(1):260.
Frnakenstein: multiple target inverse RNA folding.
Lyngsoe RB, Anderson JW, Sizikova E, Badugu A, Hyland T, Hein J.

PyRosetta 2.012 – Python-based Interface to Rosetta Molecular Modeling Suite

PyRosetta 2.012

:: DESCRIPTION

PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables a user to create custom molecular modeling algorithms with Rosetta sampling and scoring functions using Python scripting. PyRosetta is designed to make the sophisticated Rosetta molecular modeling suite accessible to a broader audience of scientists in the life sciences.

::DEVELOPER

the Gray Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Python

:: DOWNLOAD

PyRosetta

:: MORE INFORMATION

Citation

S. Chaudhury, S. Lyskov & J. J. Gray,
“PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta,”
Bioinformatics, 26(5), 689-691 (2010).

Mavric 0.8.3 – Python toolkit for Phylogenetics

Mavric 0.8.3

:: DESCRIPTION

Mavric is a python module for the manipulation and visualization of phylogenetic trees. It is also a recursive acronym for Mavric Visualizes Rick’s Cladograms :) It aims to be a user-friendly tool for manipulating phylogenetic trees on *NIX-like systems, especially Linux. As such it complements other phylogeny programs like those in the PHYLIP package, which for all their strengths currently lack a nice graphical interface.

::DEVELOPER

Rick Ree rree at oeb.harvard.edu.

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
Python

:: DOWNLOAD

Mavric

:: MORE INFORMATION