This document provides an overview of phylogenetic analysis and interpreting phylogenetic trees. It discusses: - The main goals of phylogenetic reconstruction are to describe evolutionary relationships in terms of common ancestry and represent them as branching diagrams or trees. - The three main types of evolutionary relationships are monophyly, paraphyly, and polyphyly. - Key steps in phylogenetic analysis include choosing a study group, sampling data sources, retrieving and aligning sequences, and analyzing amino acid or nucleotide data. - Interpreting phylogenetic trees involves examining relationships between terminals of interest to answer biological questions about orthology, paralogy, and monophyly, paraphyly, or polyphyly.

1. •A phylogeny is the evolutionary history of a
group of entities
•The main aim of phylogeny reconstruction is to
describe evolutionary relationships in terms of
relative recency of common ancestry.
•Represented as a branching diagram, or tree,
with branches joined by nodes and leading to
terminals at the tips of the tree
The three main types
of relationship:
• Monophyly
• Paraphyly
• Polyphyly

2. Overview of phylogenetic analysis
Choosing a study group • Survey the literature pertaining to the group of interest.
Sampling the group of
interest
• 4 sources of data for reconstructing the phylogeny of a gene family:
published sequences of characterized, gene databases, EST project
databases, and unpublished data from colleagues.
Sequence retrieval
• Sequences retrieved from BLAST searches varies depending on the size of
the gene family, and what is chosen for inclusion in further analyses will vary
accordingly.
• When sequences are retrieved from BLAST searches they are allocated an e-
score, which is an indication of the degree of similarity between the initial
sequence used for searches and the sequence retrieved.
Amino acid or nucleotide
data analysis
• Data as amino lebih banyak kemungkinan keadaan karakter dibandingkan
dengan nukleotida (20:4).
• Alignment as amino lbh mudah
Alignment
• Phylogenetic methodology relies on the assumption that the characters used
to generate trees are homologous.

3. Automatic
alignments
failed

4. Interpreting a phylogenetic tree
• Look at the strict consensus parsimony tree. A totally unresolved tree
(the branches all come out from the same node) may indicate a rapid
radiation, insufficient phylogenetic information in the original
alignment or incongruence between tree topologies.
• Compare the strict consensus parsimony and ML trees to see if they
are congruent
• Look at the relationships between the terminals of interest and see
how they answer the biological question that was originally posed in
terms of orthology and paralogy, and in terms of monophyly,
paraphyly and polyphyly.