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

2002 –

libcoevolution, a C++ library for molecular coevolution analysis by J. Dutheil, based on the 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

2002 –

libcoevolution, a C++ library for molecular coevolution analysis by J. Dutheil, based on the 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

2002 –

libcoevolution, a C++ library for molecular coevolution analysis by J. Dutheil, based on the 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

2002 –

libcoevolution, a C++ library for molecular coevolution analysis by J. Dutheil, based on the 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

2002 –

libcoevolution, a C++ library for molecular coevolution analysis by J. Dutheil, based on the 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

2002 –

libcoevolution, a C++ library for molecular coevolution analysis by J. Dutheil, based on the 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

2008 –

Several contributions by B. Boussau and L. Gu´

• eguen. Sec-
• nd paper in BMC Evol Biol! Launch of the Bio++ Help

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

2008 –

Several contributions by B. Boussau and L. Gu´

• eguen. Sec-
• nd paper in BMC Evol Biol! Launch of the Bio++ Help

Forum – First Bio++ course in Lyon – Bio++ is mentioned in the annual report of the French branch of the Free Soft- ware Fondation

2009 –

Launch of the Bio++ Development Forum – Roadmap to version 2.00 – Bio++ is being integrated in the BioLib 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

• ffer!

1 Free and Libre Software for download jdutheil@birc.au.dk Introduction to Bio++

What do you get?

Permanent

• ffer!

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

• ffer!

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 design1 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!

1Adaptation 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++