:: DESCRIPTION
Spinesis a C++ software package for genomic sequence alignment and analysis.
::DEVELOPER
The Broad Institute, Cambridge, MA
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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.
pyOpenMS provides Python-bindings for the C++ OpenMS mass spectrometric algorithm library, allowing researchers to directly access algorithms and data structures available in C++ from the interactive Python environment. pyOpenMS thus provides access to a feature-rich, open-source algorithm library for mass-spectrometry based proteomics analysis, giving the user functionality ranging from file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ and SWATH analysis tools).
DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Röst HL, Schmitt U, Aebersold R, Malmström L.
pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.
Proteomics. 2014 Jan;14(1):74-7. doi: 10.1002/pmic.201300246. PMID: 24420968.
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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
Swalign is a simple Smith-Waterman alignment implementation in C.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The BioC++ project provides an accessible and comprehensive framework of C/C++ tools and libraries for computational biology.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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
