Introduction to Bio++ Julien Dutheil jdutheil@birc.au.dk - PowerPoint PPT Presentation

Introduction to Bio++ Julien Dutheil jdutheil@birc.au.dk Bioinformatics Research Center Aarhus University June 16-18th jdutheil@birc.au.dk Introduction to Bio++

What is Bio++ ? BioC++ ? jdutheil@birc.au.dk Introduction to Bio++

What is NOT Bio++ ? BioC++ ? Characteristic #1 Bio++ is not a BioC++, it’s not a replacement for and is not incompatible with the projects supported by the Open Bioinformatics Foundation! jdutheil@birc.au.dk Introduction to Bio++

What is Bio++ ? Characteristic #2 Bio++ is a C++ library dedicated to sequence analysis, phylogenetics, population genetics and molecular evolution. It is designed for: development and test of new models / methods easy and efficient implementation of workflow analysis jdutheil@birc.au.dk Introduction to Bio++

Short history of the project libcoevolution, a C++ library for molecular coevolution analysis by J. Dutheil, based on the 2002 – SEMPHY library. Project ”SeqLib” starts with G. Deuchst under the supervision of K. Belkhir, N. Galtier and J. Dutheil. jdutheil@birc.au.dk Introduction to Bio++

Short history of the project libcoevolution, a C++ library for molecular coevolution analysis by J. Dutheil, based on the 2002 – SEMPHY library. Project ”SeqLib” starts with G. Deuchst under the supervision of K. Belkhir, N. Galtier and J. Dutheil. 2003 – libcoevolution is split into PhylLib and CoMap. jdutheil@birc.au.dk Introduction to Bio++

Short history of the project libcoevolution, a C++ library for molecular coevolution analysis by J. Dutheil, based on the 2002 – SEMPHY library. Project ”SeqLib” starts with G. Deuchst under the supervision of K. Belkhir, N. Galtier and J. Dutheil. 2003 – libcoevolution is split into PhylLib and CoMap. 2004 – S. Gaillard develops PopGenLib under the supervision of E. Bazin, N. Galtier and K. Belkhir. jdutheil@birc.au.dk Introduction to Bio++

Short history of the project libcoevolution, a C++ library for molecular coevolution analysis by J. Dutheil, based on the 2002 – SEMPHY library. Project ”SeqLib” starts with G. Deuchst under the supervision of K. Belkhir, N. Galtier and J. Dutheil. 2003 – libcoevolution is split into PhylLib and CoMap. 2004 – S. Gaillard develops PopGenLib under the supervision of E. Bazin, N. Galtier and K. Belkhir. 2005 – Various contributions from S. Gl´ emin (PopGenLib) and V. Ranwez (PhylLib). jdutheil@birc.au.dk Introduction to Bio++

Short history of the project libcoevolution, a C++ library for molecular coevolution analysis by J. Dutheil, based on the 2002 – SEMPHY library. Project ”SeqLib” starts with G. Deuchst under the supervision of K. Belkhir, N. Galtier and J. Dutheil. 2003 – libcoevolution is split into PhylLib and CoMap. 2004 – S. Gaillard develops PopGenLib under the supervision of E. Bazin, N. Galtier and K. Belkhir. 2005 – Various contributions from S. Gl´ emin (PopGenLib) and V. Ranwez (PhylLib). 2006 – First paper in BMC Bioinformatics! – C. Scornavacca de- velops tools for phylogenetic trees. jdutheil@birc.au.dk Introduction to Bio++

Short history of the project libcoevolution, a C++ library for molecular coevolution analysis by J. Dutheil, based on the 2002 – SEMPHY library. Project ”SeqLib” starts with G. Deuchst under the supervision of K. Belkhir, N. Galtier and J. Dutheil. 2003 – libcoevolution is split into PhylLib and CoMap. 2004 – S. Gaillard develops PopGenLib under the supervision of E. Bazin, N. Galtier and K. Belkhir. 2005 – Various contributions from S. Gl´ emin (PopGenLib) and V. Ranwez (PhylLib). 2006 – First paper in BMC Bioinformatics! – C. Scornavacca de- velops tools for phylogenetic trees. 2007 – N. Galtier develops bootstrap tools. Creation of Bio++ Program Suite. jdutheil@birc.au.dk Introduction to Bio++

Short history of the project Several contributions by B. Boussau and L. Gu´ eguen. Sec- ond paper in BMC Evol Biol! Launch of the Bio++ Help 2008 – Forum – First Bio++ course in Lyon – Bio++ is mentioned in the annual report of the French branch of the Free Soft- ware Fondation jdutheil@birc.au.dk Introduction to Bio++

Short history of the project Several contributions by B. Boussau and L. Gu´ eguen. Sec- ond paper in BMC Evol Biol! Launch of the Bio++ Help 2008 – Forum – First Bio++ course in Lyon – Bio++ is mentioned in the annual report of the French branch of the Free Soft- ware Fondation Launch of the Bio++ Development Forum – Roadmap to version 2.00 – Bio++ is being integrated in the BioLib 2009 – project, interfacing C++ libraries in Java, R, Perl, Python and Ruby – Second course hosted by the university of Glas- gow jdutheil@birc.au.dk Introduction to Bio++

What do you get? Permanent offer! 1 Free and Libre Software for download jdutheil@birc.au.dk Introduction to Bio++

What do you get? Permanent offer! 1 Free and Libre Software for download 2 A detailed documentation 3 A (draft!) tutorial jdutheil@birc.au.dk Introduction to Bio++

What do you get? Permanent offer! 1 Free and Libre Software for download 2 A detailed documentation 3 A (draft!) tutorial 4 A forum to ask specific questions and get help jdutheil@birc.au.dk Introduction to Bio++

That’s ALMOST for free... [Bio++] is evolution, not intelligent design 1 You are welcomed to: Report any bug you may find Improve the documentation by correcting typos, adding references... Subscribe to the forum! Help on the tutorial! Contribute some code! 1 Adaptation from Linus Torwald’s famous ”Linux is evolution, not intelligent design”. jdutheil@birc.au.dk Introduction to Bio++

Outline 1 A short introduction to Object-Orientation in Bio++ 2 Climbing up the hierarchies: Alphabets, Sequences and Containers. 3 Introducing the PopGenLib library. 4 Trees, nodes and branches: a first grasp with the PhylLib library. 5 Models for phylogenetics. 6 More complex models (with the Bio++ Program Suite). 7 Concluding remarks. jdutheil@birc.au.dk Introduction to Bio++