BEAST: Pathogen Phylogenetics

Molecular Evolutionary Analysis of Pathogens using BEAST

Tree Building 2: Maximum Likelihood, Bayesian Analysis, and Making Tree Figures

Tree Building 1: Neighbor Joining, Parsimony, and Bootstrapping

Introduction, Seq. Similarity, and BLAST introduces sequence similarity, the BLAST alignment software, and background of why similarity is used.

Survey of molecular and population mechanisms creating and maintaining genetic diversity.

Mechanisms of Evolution including mutations, chromosomal variations and genomic variations

Viral Sequence Alignment and Phylogenetics Seminar

Phylogenetics training of fours seminars - from start to finish - with slides, shell scripts, and data files

Introduction to the BEAST software for Bayesian phylogenetic analysis.

Introduction to Bayesian methods for inferring changes in population size over time form genomic data.

How to use location data for Bayesian phylodynamic analysis

Sequence assembly including starting with a clean sequence, collecting homologs, alignment and building trees

Introduction to basic sequence alignment algorithms and their uses.

Phylogenetic Tree building Parts I & II

Making Publication-Quality Trees Figures

Selection Analysis Using HyPhy

Introduction to the FASTA sequence data file format.

How to use the ClustalX program to perform multiple sequence alignment.

Neighbor-joining tree with MEGA5 shorts - including file format conversion, import, and neighbor joining tree calculations

Phylogenetic Input data File Formats