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Models and Algorithms for Genome Evolution 2013

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Cédric Chauve, Nadia El-Mabrouk, Eric Tannier:
Models and Algorithms for Genome Evolution. Springer 2013, ISBN 978-1-4471-5297-2

Emergence of Standard Algorithms

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Gene Myers:
What's Behind Blast. 3-15
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David Bryant, Jamie Kydd:
Forty Years of Model-Based Phylogeography. 17-28
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Miklós Csürös:
How to Infer Ancestral Genome Features by Parsimony: Dynamic Programming over an Evolutionary Tree. 29-45
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Cédric Chauve, Nadia El-Mabrouk, Laurent Guéguen, Magali Semeria, Eric Tannier:
Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later. 47-62
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  - books/daglib/p/BergeronS13
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Anne Bergeron, Jens Stoye:
The Genesis of the DCJ Formula. 63-81

New Lights on Current Paradigms

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Tandy J. Warnow:
Large-Scale Multiple Sequence Alignment and Phylogeny Estimation. 85-146
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Bernard M. E. Moret, Yu Lin, Jijun Tang:
Rearrangements in Phylogenetic Inference: Compare, Model, or Encode? 147-171
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Liqing Zhang, Mingming Liu, Layne T. Watson:
Status of Research on Insertion and Deletion Variations in the Human Population. 173-181
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Binhai Zhu:
A Retrospective on Genomic Preprocessing for Comparative Genomics. 183-206
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Joao Meidanis, Sophia Yancopoulos:
The Emperor Has No Caps! A Comparison of DCJ and Algebraic Distances. 207-243

Promising Directions

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David Sankoff, Chunfang Zheng:
Fractionation, Rearrangement, Consolidation, Reconstruction. 247-260
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Manuel Lafond, Krister M. Swenson, Nadia El-Mabrouk:
Error Detection and Correction of Gene Trees. 261-285
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Marília D. V. Braga, Cédric Chauve, Daniel Doerr, Katharina Jahn, Jens Stoye, Annelyse Thévenin, Roland Wittler:
The Potential of Family-Free Genome Comparison. 287-307
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Daniel E. Platt, Filippo Utro, Marc Pybus, Laxmi Parida:
Genetic History of Populations: Limits to Inference. 309-323

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