Bioinformatics for Evolutionary Biologists

Part I Problems.- 1 The Unix Command Line.- 1.1 Getting Started.- 1.2 Files, Directories, and Programs.-1.3 Scripts.- 2 Optimal Alignment.- 2.1 Keeping Score.- 2.2 Construction.- 2.3 Application.- 3 Exact Matching.- 3.1 Keyword Trees.- 3.2 Suffix Trees.- 3.3 Suffix Arrays.- 3.4 Text Compression.- 4 Fast Alignment.- 4.1 Global.- 4.2 Local.- 4.3 Glocal.- 4.4 Assembly.- 4.5 Multiple Sequences.- 5 Evolution Between Species: Phylogeny.- 5.1 Trees of Life.- 5.2 Rooted Trees.- 5.3 Unrooted Trees.- 6 Evolution within Populations.- 6.1 Descent from One or Two Parents.- 6.2 The Coalescent.- 7 Interrogating and Storing Data.- 7.1 Statistics.- 7.2 Relational Databases.- Part II Answers. .- 1 The Unix Command Line.- 1.1 Getting Started.- 1.2 Files, Directories, and Programs.- 1.3 Scripts.- 2 Optimal Alignment.- 2.1 Keeping Score.- 2.2 Construction.- 2.3 Application.- 3 Exact Matching.- 3.1 Keyword Trees.- 3.2 Suffix Trees.- 3.3 Suffix Arrays.- 3.4 Text Compression.- 4 Fast Alignment.- 4.1 Global.- 4.2 Local.- 4.3 Glocal.- 4.4 Assembly.- 4.5 Multiple Sequences.- 5 Evolution Between Species: Phylogeny.- 5.1 Trees of Life.- 5.2 Rooted Trees.- 5.3 Unrooted Trees.- 6 Evolution within Populations.- 6.1 Descent from One or Two Parents.- 6.2 The Coalescent.- 7 Interrogating and Storing Data.- 7.1 Statistics.- 7.2 Relational Databases.- A. Unix Guide.- B. Programs.- B.1 Own.- B.2 Biobox.- B.3 Third-Party.- References.- Index

Bernhard Haubold studied Natural Sciences at Cambridge University, UK and completed his DPhil in bBacterial population genetics at Oxford University, UK in 1998. After training as a Post-Doc at the Max-Planck-Institute for Chemical Ecology in Jena, Germany he worked in the biotech industry before taking on a professorship in Bioinformatics at the University of Applied Sciences, Weihenstephan, Germany in 2003. In 2008, he moved to his current post as a researcher at the Max-Planck-Institute for Evolutionary Biology in Plön, Germany. He also teaches Bioinformatics at Lübeck University. Together with Thomas Wiehe he is the author of Introduction to Computational Biology - An Evolutionary Approach, which was published by Birkhäuser in 2006.

Angelika Börsch-Haubold studied Pharmacy at Freiburg University, Germany and Pharmacology at Cambridge University, UK. She completed her DPhil in Pharmacology at Oxford University, UK in 1997, and was a junior research fellow at Linacre College, Oxford between 1997 and 1998. From 2005 to 2008, she taught various courses at the University of Applied Sciences, Weihenstephan, Germany. From 2008 to 2014 she worked as a researcher at the Max-Planck-Institute for Evolutionary Biology in Plön, Germany. She has contributed teaching material to Science in School and was involved in translating the fifth edition of The Molecular Biology of the Cell into German.