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Substitution model
Mutations, the Molecular Clock, and Models of Sequence Evolution
Phylogeny Codon Models • Last Lecture: Poor Man’S Way of Calculating Dn/Ds (Ka/Ks) • Tabulate Synonymous/Non-Synonymous Substitutions • Normalize by the Possibilities
The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing, Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme (Eds.)
A Review of Molecular-Clock Calibrations and Substitution Rates In
Relative Model Selection Can Be Sensitive to Multiple Sequence Alignment Uncertainty
Empirical Models for Substitution in Ribosomal RNA
Local and Relaxed Clocks: the Best of Both Worlds
Bayesian Codon Substitution Modelling to Identify Sources of Pathogen Evolutionary Rate Variation
Assessing the State of Substitution Models Describing Noncoding RNA Evolution
Effects of Parameter Estimation on Maximum-Likelihood Bootstrap Analysis
Evolutionary and Functional Lessons from Human-Specific Amino-Acid
Empirical Models for Substitution in Ribosomal RNA
The Molecular Clock As a Tool for Understanding Host-Parasite Evolution
A Metaanalysis of Bat Phylogenetics and Positive Selection Based on Genomes and Transcriptomes from 18 Species
Genome-Wide Signatures of Convergent Evolution in Echolocating Mammals
Relative Evolutionary Rates in Proteins Are Largely Insensitive to the Substitution Model
Using the Mutation-Selection Framework to Characterize Selection on Protein Sequences
Selection of Evolutionary Models for Phylogenetic Hypothesis Testing Using Parametric Methods
Top View
Using Structural Information in Modeling and Multiple Alignments for Phylogenetics
Reconstruction of Phylogenetic Trees
Lecture 9 Dating Phylogenetic Trees
Evolutionary Approaches to Sequence Alignment
How to Build a Phylogenetic Tree
BINF6201/8201 Protein Substitution Models
The Effect of RNA Substitution Models on Viroid and RNA Virus Phylogenies
Multiple Sequence Alignment Algorithms for the Phylogenic Analysis of Chloroplast DNA
Mutation Rate Is Linked to Diversification in Birds
The Effect of RNA Substitution Models on Viroid and RNA Virus Phylogenies
Inferring Evolutionary Timescales Without Independent Timing
Model Selection in Phylogenetics
Bridging the Gaps in Statistical Models of Protein Alignment
Modelteller: Model Selection for Optimal Phylogenetic
Bayesian Phylogenetics Using an RNA Substitution Model Applied to Early Mammalian Evolution
Phylogenetic Analysis
Adenine•Cytosine Substitutions Are an Alternative Pathway of Compensatory Mutation in Angiosperm ITS2
How to Select Best Substitution Model by Kakusan4/Aminosan?
A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment And
Models of Amino Acid Substitution and Applications to Mitochondrial Protein Evolution
Section 1 of Speed's Notes on Evolution and Phylogeny
EBLV-1) Emphasize a Higher Genetic Resolution and Spatial Segregation for Sublineage 1A
Mitochondrial Substitution Rates Estimation for Molecular Clock
Phylogenetic Analyses of Alignments with Gaps
The Ranging of Amino Acids Substitution Matrices of Various
The Effects of Nucleotide Substitution Model Assumptions on Estimates of Nonparametric Bootstrap Support
Optimal Multiple Sequence Alignment
Rates of Viral Evolution Are Linked to Host Geography in Bat Rabies
New Candidate Species Most Closely Related to Penguins
Genetic Distances and Nucleotide Substitution Models
A Guide to Phylogenetic Reconstruction Using Heterogeneous Models—A Case Study from the Root of the Placental Mammal Tree
Taming the Beast Workshop Molecular Evolution Models
Nucleotides Substitution Model & Evolution
Amino Acid Coevolution Induces an Evolutionary Stokes Shift
CHD Genes: a Reliable Marker for Bird Populations and Phylogenetic Analysis? Case Study of the Superfamily Sylvioidea (Aves: Passeriformes)