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Phylogenetics in the Genomic Era |
Full Book |
Part 1: Phylogenetic analyses in the genomic era
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A gentle Introduction to Probabilistic Evolutionary Models |
1.1:1--1.1:21 |
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Efficient Maximum Likelihood Tree Building Methods |
1.2:1--1.2:18 |
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Using RAxML-NG in Practice |
1.3:1--1.3:25 |
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The Bayesian Approach to Molecular Phylogeny |
1.4:1--1.4:17 |
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PhyloBayes: Bayesian Phylogenetics Using Site-heterogeneous Models |
1.5:1--1.5:16 |
Part 2: Data quality, model adequacy
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To What Extent Current Limits of Phylogenomics Can Be Overcome? |
2.1:1--2.1:34 |
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Strengths and Limits of Multiple Sequence Alignment and Filtering Methods |
2.2:1--2.2:36 |
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Accurate Alignment of (Meta)barcoding Data Sets using MACSE |
2.3:1--2.3:31 |
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Orthology: Definitions, Prediction, and Impact on Species Phylogeny Inference |
2.4:1--2.4:14 |
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Ancestral Genome Organization as a Diagnosis Tool for Phylogenomics |
2.5:1--2.5:19 |
Part 3: Resolving phylogenomic conflicts
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The Sources of Phylogenetic Conflicts |
3.1:1--3.1:23 |
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Reconciling Gene trees with Species Trees |
3.2:1--3.2:23 |
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The Multi-species Coalescent Model and Species Tree Inference |
3.3:1--3.3:21 |
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The Concatenation Question |
3.4:1--3.4:23 |
Part 4: Functional evolutionary genomics
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Phylogenomics and Genome Annotation |
4.1:1--4.1:26 |
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Molecular Evolution and Gene Function |
4.2:1--4.2:20 |
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The Expression Comparison Tool in Bgee |
4.3:1--4.3:4 |
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Substitution Rate Analysis and Molecular Evolution |
4.4:1--4.4:21 |
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Detecting Adaptation from Multi-species Protein-coding DNA Sequence Alignments Alignments |
4.5:1--4.5:18 |
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The Nature and Phylogenomic Impact of Sequence Convergence |
4.6:1--4.6:17 |
Part 5: Phylogenomic applications
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Inferring the Timescale of Phylogenetic Trees from Fossil Data |
5.1:1--5.1:18 |
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Estimating a Time-calibrated Phylogeny of Fossil and Extant Taxa using RevBayes |
5.2:1--5.2:23 |
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Efficiently Analysing Large Viral Data Sets in Computational Phylogenomics |
5.3:1--5.3:43 |
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BEAGLE 3 High-performance Computational Library for Phylogenetic Inference |
5.4:1--5.4:9 |
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Species Delimitation |
5.5:1--5.5:18 |
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A Tutorial on the Use of BPP for Species Tree Estimation and Species Delimitation |
5.6:1--5.6:16 |
