LIBFBAT 0.5.1 – C++ library for Family Based Association Testing

LIBFBAT 0.5.1

:: DESCRIPTION

LIBFBAT programming library s robust both to genotyping errors and missing genotypes. The underlying method consists in considering an incomplete data model where the true unobserved genotypes produce the observed one through an explicit genotyping error model.

::DEVELOPER

LIBFBAT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OsX/ Linux
  • C++ Compiler

:: DOWNLOAD

LIBFBAT

:: MORE INFORMATION

Citation

Gregory Nuel, Yousri Slaoui and Vincent Miele,
libfbat: a C++ library for family based association testing,
Proceedings of JOBIM, 2008

NGS++ 1.2.1 – C++ library for Manipulating Next Generation Sequencing data

NGS++ 1.2.1

:: DESCRIPTION

NGS++ is a programming library in C++11 specialized in manipulating both next-generation sequencing (NGS) datasets and genomic information files.

::DEVELOPER

NGS++ team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

 NGS++

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 1;29(15):1893-4. doi: 10.1093/bioinformatics/btt312. Epub 2013 Jun 4.
NGS++: a library for rapid prototyping of epigenomics software tools.
Nordell Markovits A1, Joly Beauparlant C, Toupin D, Wang S, Droit A, Gevry N.

libStatGen 1.0.14 – C++ Library for Handling and Analyzing Next Generation Sequencing and Genotyping Data

libStatGen 1.0.14

:: DESCRIPTION

libStatGen is a C++ library and tools for handling and analyzing next generation sequencing and genotyping data.The library contains easy-to-use APIs for developing tools for processing and analyzing next generation sequencing and genotyping data. Allows easy processing of SAM/BAM, GLF, and FASTQ

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler
:: DOWNLOAD

 libStatGen

:: MORE INFORMATION

SeqAn 2.2.0 – Open Source C++ Library of Sequences Analysis

SeqAn 2.2.0

:: DESCRIPTION

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance.

::DEVELOPER

SeqAn Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

 SeqAn

:: MORE INFORMATION

Citation

SeqAn an efficient, generic C++ library for sequence analysis.
Döring A, Weese D, Rausch T, Reinert K.
BMC Bioinformatics. 2008 Jan 9;9:11.

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

fwdpp 0.2.9 – C++ Template Library for Efficient Forward-Time Population Genetic Simulation

fwdpp 0.2.9

:: DESCRIPTION

fwdpp is a C++ template library for developing forward-time simulations under population- and quantitative- genetic models.

::DEVELOPER

Thornton Lab at UC Irvine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 fwdpp

:: MORE INFORMATION

Citation

Thornton, K. R. (2014)
A C++ template library for efficient forward-time population genetic simulation of large populations.
Genetics 98:157-166 PMID: 24950894,

libGenome 1.3.1 – C library for Developing Sequence Analysis

libGenome 1.3.1

:: DESCRIPTION

libGenome is a freely available toolkit for developing sequence analysis software in C++. It is intended to take the hassle out of performing common tasks on genetic sequence and annotation data.

::DEVELOPER

Genome Evolution Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/  Windows
  • C/C++ Compiler

:: DOWNLOAD

 libGenome

:: MORE INFORMATION

libScopes – C++ Library for Calculation of Biochemical Scopes

libScopes

:: DESCRIPTION

libScopes can be used to predict the network behavior for metabolic, signaling and gene regulatory networks. The library can calculate biochemical scopes based on give biochemical reaction networks and predefined initial conditions

::DEVELOPER

Theoretical Biophysics Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux
  • C++ Compiler

:: DOWNLOAD

 libScopes 

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 15;28(4):557-63. doi: 10.1093/bioinformatics/btr697. Epub 2011 Dec 22.
Modeling mechanistic biological networks: an advanced Boolean approach.
Handorf T1, Klipp E.

GFMCMC 1.0 – C Library of GLUT for Markov Chain Monte Carlo

GFMCMC 1.0

:: DESCRIPTION

GFMCMC (GLUT for Markov Chain Monte Carlo) This is a library of C code that I wrote to use the (relatively) platform-independent OpenGL Utilities Toolkit (GLUT) for rendering pictures of one’s MCMC simulation in real time. It is essentially a small application programming interface.

::DEVELOPER

Eric C. Anderson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • C Compiler

:: DOWNLOAD

 GFMCMC

:: MORE INFORMATION

Alnpack 2.1 – C++ Library for Pairwise Local Alignment

Alnpack 2.1

:: DESCRIPTION

Alnpack is a set of programs and a C++ library for pairwise local alignment of DNA or protein sequences using Smith-Waterman algorithm.

:: DEVELOPER

Genetic Information Research Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • C++ compiler

:: DOWNLOAD

  Alnpack

:: MORE INFORMATION

Citation:

Farrar M.
Striped Smith-Waterman speeds database searches six times over other SIMD implementations.
Bioinformatics. 2007 Jan 15;23(2):156-61. Epub 2006 Nov 16.