Tag: Python

eSBMTools 1.04 – Python tools for enhanced Native Structure-based Modeling

eSBMTools 1.04

:: DESCRIPTION

eSBMTools: python tools that assist the setup and evaluation of native structure-based simulations of proteins and nucleic acids, both at the Cα and all-atom level. The tools interface with GROMACS and support its standard output formats. Information from other sources like bioinformatics or experimental data can be added to the standard native structure-based model (SBM).

::DEVELOPER

eSBMTools team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Python

:: DOWNLOAD

 eSBMTools

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Nov 1;29(21):2795-6. doi: 10.1093/bioinformatics/btt478. Epub 2013 Sep 9.
eSBMTools 1.0: enhanced native structure-based modeling tools.
Lutz B1, Sinner C, Heuermann G, Verma A, Schug A.

Biopython 1.79 – Tools for Biological Computation written in Python

Biopython 1.79

:: DESCRIPTION

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.

::DEVELOPER

Biopython Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Biopython

:: MORE INFORMATION

Citation:

Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, and de Hoon MJ.
Biopython: freely available Python tools for computational molecular biology and bioinformatics.
Bioinformatics 2009 Jun 1; 25(11) 1422-3. doi:10.1093/bioinformatics/btp163 pmid:19304878.

InfoTrim – DNA Read Quality Trimmer using Entropy Created with Python

InfoTrim

:: DESCRIPTION

InfoTrim is a DNA read quality trimmer based on the Trimmomatic maximum information criterion model.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

InfoTrim

:: MORE INFORMATION

Citation

InfoTrim: A DNA read quality trimmer using entropy
2017 IEEE 7th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)

Illuminate 0.6.5 – Analytics toolkit in Python for Illumina HiSeq and MiSeq metrics

Illuminate 0.6.5

:: DESCRIPTION

Illuminate parses the metrics binaries that result from Illumina sequencer runs, and provides usable data in the form of python dictionaries and dataframes. Intended to emulate the output of Illumina SAV, illuminate allows you to print sequencing run metrics to the command line as well as work with the data programmatically.

::DEVELOPER

Naomi Most

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Python

:: DOWNLOAD

 Illuminate

:: MORE INFORMATION

Omics Integrator 0.3.1 – Python Scripts for Analyzing Diverse Forms of ‘omic’ data

Omics Integrator 0.3.1

:: DESCRIPTION

Omics Integrator is package comprised of command-line tools designed to integrate high-throughput datasets such as gene expression, phospho-proteomic data and the results from genetic screens.

::DEVELOPER

The Fraenkel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

  Omics Integrator

:: MORE INFORMATION

Citation

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package.
Tuncbag N, Gosline SJ, Kedaigle A, Soltis AR, Gitter A, Fraenkel E.
PLoS Comput Biol. 2016 Apr 20;12(4):e1004879. doi: 10.1371/journal.pcbi.1004879

ngSeqUtils 1.2.1 – Utility Scripts in Python for Handling Next Generation Sequencing data

ngSeqUtils 1.2.1

:: DESCRIPTION

ngSeqUtils is a small collection of scripts to assist data analysis of Next Generation Sequencing data and handle wig, bigwig, and gff files in python.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 ngSeqUtils

 :: MORE INFORMATION

ProDy 1.10.10 – Python package for Analysis and Modeling of Protein Structural Dynamics

ProDy 1.10.10

:: DESCRIPTION

ProDy is a free and open-source Python package for analysis and modeling of protein structural dynamics. It allows for efficient analysis of large datasets and is suitable for development or prototyping of structure-based analysis and modeling software.

::DEVELOPER

Bahar lab

:: SCREENSHOTS

N/A

::  REQUIREMENTS

:: DOWNLOAD

 ProDy

:: MORE INFORMATION

Citation:

Bakan A, Meireles LM, Bahar I
ProDy: Protein Dynamics Inferred from Theory and Experiments
Bioinformatics 2011 27(11):1575-1577.

pyHIVE 1.0.8 – Health-related image visualization and engineering system using Python

pyHIVE 1.0.8

:: DESCRIPTION

pyHIVE was implemented as an image processing system, providing five widely used image feature engineering algorithms.

::DEVELOPER

Health Informatics Lab (HILab)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Python

:: DOWNLOAD

pyHIVE

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2018 Nov 26;19(1):452. doi: 10.1186/s12859-018-2477-7.
pyHIVE, a health-related image visualization and engineering system using Python.
Zhang R, Zhao R, Zhao X, Wu D, Zheng W, Feng X, Zhou F.

wgd – Whole Genome Duplication analysis in Python

wgd

:: DESCRIPTION

wgd is a Python package and command line interface (CLI) for the analysis of whole genome duplications (WGDs). wgd implements methods for constructing Ks distributions starting from a CDS fasta file, tools for intra-genomic synteny analysis and methods for modeling and visualizing Ks distributions.

::DEVELOPER

Van de Peer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Python

:: DOWNLOAD

wgd

:: MORE INFORMATION

Citation:

Zwaenepoel, A., and Van de Peer, Y.
wgd – simple command line tools for the analysis of ancient whole genome duplications.
Bioinformatics., bty915, https://doi.org/10.1093/bioinformatics/bty915

cyvcf2 v0.11.5 – Fast, Flexible Variant Analysis with Python

cyvcf2 v0.11.5

:: DESCRIPTION

cyvcf2 is a Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • Python

:: DOWNLOAD

cyvcf2

:: MORE INFORMATION

Citation:

Bioinformatics. 2017 Jun 15;33(12):1867-1869. doi: 10.1093/bioinformatics/btx057.
cyvcf2: fast, flexible variant analysis with Python.
Pedersen BS, Quinlan AR

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