Bio++ 2.4.1 – C++ Libraries for Bioinformatics

Bio++ 2.4.1

:: DESCRIPTION

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is fully Object Oriented and is designed to be both easy to use and computer efficient.

::DEVELOPER

Dr Julien Y. Dutheil

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

Bio++

:: MORE INFORMATION

Citation:

Dutheil J, Gaillard S, Bazin E, Glémin S, Ranwez V, Galtier N, Belkhir K.
Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics.
BMC Bioinformatics. 2006 Apr 4;7:188.

OpenMS / TOPP / TOPPAS 2.0.0 – C++ Framework for Proteomics

OpenMS / TOPP / TOPPAS 2.0.0

:: DESCRIPTION

OpenMS is an open-source software C++ library for LC/MS data management and analyses. It offers an infrastructure for the development of mass spectrometry related software.

 TOPP (The OpenMS Proteomics Pipeline) is a pipeline for the analysis of HPLC/MS data. It consists of several small applications that can be chained to create analysis pipelines tailored for a specific problem. We are currently at well over 40 tools, covering everything from basic signal processing of MS data, to wrapping MS/MS search engines, map alignment, retention time prediction, identification mapping/filtering and much more.

TOPPAS (The TOPP Pipeline Assistant ) is a graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction thus reduces to simple drag-and-drop of analysis tools and adding connections in between. As building blocks, you can use all TOPP tools and UTILS shipped with OpenMS. Additionally we provide wrappers for external tools. To add your own external tool, all you need to do is to write a little script.

DEVELOPER

OpenMS Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows  / MacOsX
  • C++ Compiler

:: DOWNLOAD

 OpenMS / TOPP / TOPPAS

:: MORE INFORMATION

Citation:

TOPPAS: A Graphical Workflow Editor for the Analysis of High-Throughput Proteomics Data.
Junker J, Bielow C, Bertsch A, Sturm M, Reinert K, Kohlbacher O.
J Proteome Res. 2012 Jul 6;11(7):3914-20. Epub 2012 May 24.

OpenMS and TOPP: open source software for LC-MS data analysis.
Bertsch A, Gröpl C, Reinert K, Kohlbacher O.
Methods Mol Biol. 2011;696:353-67.

EggLib 2.1.10 – C++/Python library and program package for Evolutionary Genetics and Genomics

EggLib 2.1.10

:: DESCRIPTION

EggLib is a C++/Python library and program package for evolutionary genetics and genomics. Main features are sequence data management, sequence polymorphism analysis, coalescent simulations and Approximate Bayesian Computation.

::DEVELOPER

EggLib team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Python/C++ Compiler

:: DOWNLOAD

 EggLib

:: MORE INFORMATION

Citation

De Mita S. and M. Siol. 2012.
EggLib: processing, analysis and simulation tools for population genetics and genomics.
BMC Genet. 13:27.

Bio C# 1.0 – C# Class Library for Bioinformatics

Bio C# 1.0

:: DESCRIPTION

Bio C# contains classes for handling fasta IO, Blast-search (using an own algorithm), local and global alignments, quality sequence IO, statistics (Mann-Whitney, Poisson Distribution), distribution of features along chromosomes, SNP-identification, gene expression statistics, 454-sequence handling, microsatellite search and basic sequence statistics

::DEVELOPER

Robert Kofler

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • .Net Framework 2.0

:: DOWNLOAD

 Bio C#

:: MORE INFORMATION

BioC++ 0.3 – C++ Computational Libraries for Bioinformatics

BioC++ 0.3

:: DESCRIPTION

The BioC++ project provides an accessible and comprehensive framework of C/C++ tools and libraries for computational biology.

::DEVELOPER

Hongyu Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 BioC++

:: MORE INFORMATION

NCL 2.1.18 – NEXUS C++ Class Library

NCL 2.1.18

:: DESCRIPTION

The NCL  (Nexus Class Library) is a C++ library for interpreting data files created according to the NEXUS file format used in phylogenetic systematics and molecular evolution.

::DEVELOPER

The Holder Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OsX / Linux / Windows
  • C++ Compiler

:: DOWNLOAD

  NCL

:: MORE INFORMATION

Citation:

Bioinformatics. 2003 Nov 22;19(17):2330-1.
NCL: a C++ class library for interpreting data files in NEXUS format.
Lewis PO.

Spines 1.15 – C++ Software Package for Genomic Sequence Alignment and Analysis

Spines 1.15

:: DESCRIPTION

Spinesis a C++ software package for genomic sequence alignment and analysis.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

   Spines

:: MORE INFORMATION

Citation

Grabherr MG, Russell P, Meyer M, Mauceli E, Alfoldi J, Di Palma F, Lindblad-Toh K.
Genome-wide synteny through highly sensitive sequence alignment: Satsuma.
Bioinformatics. 2010 May 1;26(9):1145-51. Epub 2010 Mar 5

PDBlib 2.2 – C++ Macromolecular Class Library

PDBlib 2.2

:: DESCRIPTION

PDBlib is an extensible object oriented class library, written in C++ for representing the 3-dimensional structure of biological macromolecules. The library models the structural features of proteins,DNA,RNA and complexes thereof, at a level of detail on a par with which can be parsed from a Brookhaven Protein Data Bank (PDB) entry. However, the memory resident representation of the macromolecule is independant of the PDB entry, and can be obtained from other sources such as relational, and object-oriented databases.

::DEVELOPER

the Bourne Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • C++ Complier

:: DOWNLOAD

 PDBlib

:: MORE INFORMATION

Citation:

W.Chang, I.N.Shindyalov, C.Pu, & P.E.Bourne,
Design and Application of PDBlib, a C++ Macromolecular Class Library.
Comput Appl Biosci (1994) 10(6), 575-586.

Segtrack – C++ & MatLab Library for Image Tracking & Segmentation

Segtrack

:: DESCRIPTION

Segtrack is a library of MATLAB functions useful for prepocessing, segmenting, tracking, postprocessing, and other tasks used for treating biological image data. See the html main_index file included in the dowload package for more details.

::DEVELOPER

Scientific Inference Systems Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • MATLAB

:: DOWNLOAD

Segtrack

:: MORE INFORMATION

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.

contact:
T.Bacarian
tbacaria@uci.edu