table-of-contents - Phylogenetics in the Genomic Era

Phylogenetics in the Genomic Era
Celine Scornavacca, Frédéric Delsuc, Nicolas Galtier

Full Book

Part 1: Phylogenetic analyses in the genomic era

A gentle Introduction to Probabilistic Evolutionary Models Tal Pupko, Itay Mayrose	1.1:1--1.1:21
Efficient Maximum Likelihood Tree Building Methods Alexandros Stamatakis, Alexey M. Kozlov	1.2:1--1.2:18
Using RAxML-NG in Practice Alexey M. Kozlov, Alexandros Stamatakis	1.3:1--1.3:25
The Bayesian Approach to Molecular Phylogeny Nicolas Lartillot	1.4:1--1.4:17
PhyloBayes: Bayesian Phylogenetics Using Site-heterogeneous Models Nicolas Lartillot	1.5:1--1.5:16

Part 2: Data quality, model adequacy

To What Extent Current Limits of Phylogenomics Can Be Overcome? Paul Simion, Frédéric Delsuc, Herve Philippe	2.1:1--2.1:34
Strengths and Limits of Multiple Sequence Alignment and Filtering Methods Vincent Ranwez, Nathalie Chantret	2.2:1--2.2:36
Accurate Alignment of (Meta)barcoding Data Sets using MACSE Frédéric Delsuc, Vincent Ranwez	2.3:1--2.3:31
Orthology: Definitions, Prediction, and Impact on Species Phylogeny Inference Rosa Fernández, Toni Gabaldon, Christophe Dessimoz	2.4:1--2.4:14
Ancestral Genome Organization as a Diagnosis Tool for Phylogenomics Eric Tannier, Adelme Bazin, Adrián Davín, Laurent Guéguen, Sèverine Bérard, Cedric Chauve	2.5:1--2.5:19

Part 3: Resolving phylogenomic conflicts

The Sources of Phylogenetic Conflicts Dominik Schrempf, Gergely Szöllősi	3.1:1--3.1:23
Reconciling Gene trees with Species Trees Bastien Boussau, Celine Scornavacca	3.2:1--3.2:23
The Multi-species Coalescent Model and Species Tree Inference Bruce Rannala, Scott V. Edwards, Adam Leaché, Ziheng Yang	3.3:1--3.3:21
The Concatenation Question David Bryant, Matthew W. Hahn	3.4:1--3.4:23

Part 4: Functional evolutionary genomics

Phylogenomics and Genome Annotation Anamaria Necsulea	4.1:1--4.1:26
Molecular Evolution and Gene Function Marc Robinson-Rechavi	4.2:1--4.2:20
The Expression Comparison Tool in Bgee Marc Robinson-Rechavi, Valentine Rech de Laval, Frédéric B. Bastian, Julien Wollbrett, Phantom (the) Bgee Team	4.3:1--4.3:4
Substitution Rate Analysis and Molecular Evolution Lindell Bromham	4.4:1--4.4:21
Detecting Adaptation from Multi-species Protein-coding DNA Sequence Alignments Alignments Christine Lowe, Nicolas Rodrigue	4.5:1--4.5:18
The Nature and Phylogenomic Impact of Sequence Convergence Zhengting Zou, Jianzhi Zhang	4.6:1--4.6:17

Part 5: Phylogenomic applications

Inferring the Timescale of Phylogenetic Trees from Fossil Data Walker Pett, Tracy A. Heath	5.1:1--5.1:18
Estimating a Time-calibrated Phylogeny of Fossil and Extant Taxa using RevBayes Joëlle Barido-Sottani, Joshua A. Justison, April M. Wright, Rachel C.M. Warnock, Walker Pett, Tracy A. Heath	5.2:1--5.2:23
Efficiently Analysing Large Viral Data Sets in Computational Phylogenomics Anna Zhukova, Olivier Gascuel, Sebastián Duchene, Daniel Ayres, Philippe Lemey, Guy Baele	5.3:1--5.3:43
BEAGLE 3 High-performance Computational Library for Phylogenetic Inference Daniel Ayres, Philippe Lemey, Guy Baele, Marc A Suchard	5.4:1--5.4:9
Species Delimitation Bruce Rannala, Ziheng Yang	5.5:1--5.5:18
A Tutorial on the Use of BPP for Species Tree Estimation and Species Delimitation Tomáš Flouri, Bruce Rannala, Ziheng Yang	5.6:1--5.6:16