Skip to Main content Skip to Navigation

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