Concept of distance, parsimony and likelihood methods; cladistics and ontology
Phylogenetic tree
Graphical representation of the evolutionary history of biological sequences that allows visualizing the evolutionary relationships between them
Phylogenetic tree
Branching lines represent evolutionary history and relatedness of different groups of organisms
Endpoints of branches represent present-day species or sequences (taxa or operational taxonomic units, OTUs)
Connecting points where two branches come together are nodes, representing inferred common ancestors
Root node represents the common ancestor of all members of the tree
Types of phylogenetic trees
Rooted (have a specified root node)
Unrooted (no specified root node, show only branching pattern)
Cladogram (unscaled, shows only branching pattern)
Phylogram (scaled, shows branching pattern and evolutionary divergence)
Phylogenetic tree construction methods
1. Distance-based (UPGMA, Neighbor-Joining)
2. Character-based (Maximum Parsimony, Maximum Likelihood)
UPGMA
Simplest distance-based method that constructs a rooted phylogenetic tree using sequential clustering
Neighbor-Joining
Most widely used distance-based method, does not assume molecular clock and produces unrooted tree
Maximum Parsimony
Character-based method that attempts to reduce branch length by minimizing evolutionary changes required between sequences
Maximum Likelihood
Character-based method that estimates probability of each nucleotide position in a sequence and calculates cumulative probability for branches of a bifurcating tree
Genome annotation
Principles of genome annotation, annotation tools and resources, measuring predictive accuracy
