Phylogenetic Analysis
Dayong Guo
Introduction
•Phylogenetics is the study of evolutionary relatedness among various
species, populations, or among a set of sequences.
•Besides the study of morphology or phenotype with traditional
definitions and concepts, molecular analysis with modern computational
tools has shown their unique strength in phylogenetics since the DNA,
RNA or protein sequence data are naturally discretely defined.
•Several computational algorithms have been developed to build
phylogenetic trees with the input of multiple sequences. The most
commonly used types of algorithms include distance-matrix methods (e.g.
neighbor-joining), maximum parsimony, maximum likelihood and
Bayesian inference, etc.
•The PHYLIP (PHYLogeny Inference Package, Felsenstein) is one of the
most popular tools for phylogenetic analysis. It includes parsimony,
distance matrix and likelihood methods.
Method and Tool
• Datasets
1) Four artificially made, short and simple
sequences (textbook page 303)
2) Four real protein sequences (Bone
Morphogenetic Protein 2 from human, mouse,
rat and frog)
• Tools
1) Use ClustalW as the aligment generator.
2) Use PHYLIP to generate phylogenetic trees
(distance method, parsimony method)
Results 1
Alignment by CLUSTALW
4
20
SeqC
ACGCATTGAA
SeqD
ACACATTGAG
SeqA
ACGCGTTGGG
SeqB
ACGCGTTGGG
From distance method
(Fitch-Margoliash algorithm)
TGATGATAAT
TGATAATAAT
CGATGGCAAC
CGACGGTAAT
From parsimony method
(Detailed processes not shown)
Result 2
1)
2)
3)
4)
Four sequences of BMP2
Alignment generated by CLUSTALW
Download PHYLIP and install
Use protdist.exefitch.exe as an
example of distance method; Or, use
protpars.exe as an example of
parsimony method
5) Drawtree.exe
Discussion
• Distance tree and parsimony tree are
different for the BMP2 dataset. It could be
result from relatively lower homology btw
frog and other species.
Distance tree
Parsimony tree
Discussion (cont)
• The PHYLIP program set includes multiple
algorithms and options providing
convenience and flexibility. And, different
versions enable performance on various
OS platforms.
• However, the text-based interface is not
friendly. And, there is no online service.