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The following sections are included: Introduction Types of Tree Building Methods Tree Building with an Objective Function Constructors Heuristics n-optim Subtree pruning and regrafting (SPR) Tree bisection reconnection (TBR) Reduce best-fitting subtree (RBFS) Tree fusing (TF) Least Squares Tree Construction Least Squares Tree Function in Darwin Time Comparison with PAUP Methods Results RBFS Heuristic Subtree index Subtree substitution Outlook References

The following sections are included: Introduction Homology and Homoplasy: Look-alikes are Not Necessarily Closely Related Characters and Their States Homology — A Phylogenetic Hypothesis Ancestral or Derived — Qualifying the State of a Character Homoplasy — Pitfall in Phylogenetics Molecular Phylogenetics Gene Duplication vs. Speciation, Paralogy vs. Orthology Sequence Alignment — A Homology Hypothesis Evolutionary Time Evolutionary distance and the course of time Time and time again: paleontology and molecular evolution Micromutations and the molecular clock Tree Reconstitution The Tree Graph Model — Transmission of Phylogenetic Information Numerical Taxonomic Phenetics (NTP) The neighbor joining algorithm A common NTP artefact Cladistic Maximum Parsimony (CMP) Methods Symplesiomorphy, synapomorphy, and autapomorphy Cladistic maximum parsimony (CMP) and character compatibility (CC) methods CMP common artefacts Probabilistic Methods Searching for an Optimal Tree in a Large, Populated Space The number of possible phylogenetic trees The branch-and-bound algorithm Heuristic methods in tree reconstruction A rapid maximum likelihood method: RAxML Creating consensus trees Estimating tree robustness Recommended, Acceptable, and Unacceptable Groupings of Taxons Paraphylon — Acceptable with caveat Convergence and reversion polyphylons — Unacceptable Uses of Phylogenetics in Molecular Biology Prediction of Gene Function Advanced Phylogenetic Analyses and New Directions Phylogenetics Resources References

The following sections are included: Introduction The Easy Part: The Evolution of Gene Sequences Rapid Overview of Bioinformatics Involved The Importance of Duplication and Loss Why don't flies have retinoic acid receptors? Why do humans have three retinoic acid receptors? Biased gene loss after whole-genome duplication Developing Bioinformatic Tools for Evo-Devo Defining Homology for Bioinformatics Modeling Homology Relationships Bgee, a Database for Gene Expression Evolution Conclusion Acknowledgments References