BiopLib 3.10 / BiopTools 1.9 – C Programming Library and Toolset for Manipulating Protein Structure.

BiopLib 3.10 / BiopTools 1.9

:: DESCRIPTION

BiopLib is a library of C routines for general programming and handling protein structure

BiopTools is a set of command line tools written in C and making use of the BiopLib library for manipulation of protein structure and sequence

::DEVELOPER

Andrew C.R. Martin’s Bioinformatics Group at UCL

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • C Compiler

:: DOWNLOAD

 BiopLib , BiopTools

:: MORE INFORMATION

Citation

BiopLib and BiopTools – a C programming library and toolset for manipulating protein structure.
Porter CT, Martin AC.
Bioinformatics. 2015 Aug 30. pii: btv482.

PDBest 1.40 – Manipulating and Enhancing Protein Structures

PDBest 1.40

:: DESCRIPTION

PDBest (PDB Enhanced Structures Toolkit)  is a freely available platform for manipulating, filtering and normalizing biomolecules in Protein Data Bank (PDB) and mmCIF structure files.

::DEVELOPER

PDBest team , the Bioinformatics and System Laboratory (LBS) at Universidade Federal de Minas Gerais, Brazil.

:: SCREENSHOTS

PDBest

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX

:: DOWNLOAD

 PDBest

:: MORE INFORMATION

Citation

PDBest: a user-friendly platform for manipulating and enhancing protein structures.
Gonҫalves WR, Gonҫalves-Almeida VM, Arruda AL, Meira W Jr, da Silveira CH, Pires DE, de Melo-Minardi RC.
Bioinformatics. 2015 Apr 24. pii: btv223

gffread 0.94f – Filtering, Converting and Manipulating GFF files

gffread 0.94f

:: DESCRIPTION

The program gffread can be used to validate, filter, convert and perform various other operations on GFF (General Feature Format) files.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 gffread

:: MORE INFORMATION

vcflib 1.0.0 – C++ Library for Parsing and Manipulating VCF files

vcflib 1.0.0

:: DESCRIPTION

vcflib is a simple C++ library for parsing and manipulating Variant Call Format (VCF) files, + many command-line utilities

::DEVELOPER

Erik Garrison erik.garrison@bc.edu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOSX
  • C++ Compiler

:: DOWNLOAD

  vcflib

:: MORE INFORMATION

DBToolkit 4.2.3 – Manipulating fasta Sequence Databases

DBToolkit 4.2.3

:: DESCRIPTION

The dbtoolkit application enables easy manipulation of fasta sequence database in a user-friendly environment. Sequence databases can be merged, shuffled, truncated, etc… Furthermore, for more experienced users, the Java API provides a well documented and easy-to-use environment for customized fasta database manipulations.

::DEVELOPER

Computational Omics and Systems Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 DBToolkit

:: MORE INFORMATION

Citation

Martens et al.
DBToolkit: processing protein databases for peptide-centric proteomics.
Bioinformatics (2005) vol. 21 (17) pp. 3584-5

Pysam 0.8.2.1 – Python module for Reading and Manipulating Sam files

Pysam 0.8.2.1

:: DESCRIPTION

Pysam is a python module for reading and manipulating Sam files.

::DEVELOPER

Computational Genomics: Analysis and Training (GCAT)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python
:: DOWNLOAD

 Pysam

:: MORE INFORMATION

mozCellML 0.3.1 – Utility for Manipulating initial conditions and integrating CellML models

mozCellML 0.3.1

:: DESCRIPTION

mozCellML is a Mozilla based CellML tool. It can be used to edit boundary conditions, integrate models(using a Runge-Kutta method), and fit parameters to models(using Levenberg-Marquardt).

::DEVELOPER

mozCellML Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 mozCellML 

:: MORE INFORMATION