MIT School of Bioengineering Sciences and Research
(A Constituent unit of MIT ADT University)
Basic Concepts In Bioinformatics / BI301
Module06
Taxonomy and phylogeny
Course Coordinator: Dr. Sanket P. Bapat / Dr. Priyanka Nath
Mail ID: [Link]@[Link] | [Link]@[Link]
Disclaimer:
The content delivered here should be considered of utmost importance. However, it is
to be noted that, this material is not Stand-alone material for the fulfilment of the
course syllabus. The content in this presentation should only be used as an aid to
learning.
Books and other resources provided are suggested to be referred for exhaustive
understanding.
MITBIO/MITADT University
Syllabus:
Module 6:
Taxonomy and phylogeny
Phylogenetic analysis algorithms such as Maximum Parsimony,
UPGMA, Transformed Distance, Neighbors-Relation, Neighbor-
Joining; Probabilistic models of evolution and Maximum likelihood
algorithm, Bootstrapping method, use of tools such as Phylip, Mega,
PAUP
MITBIO/MITADT University
Objective/Learning Outcome:
CO1 Understanding the basics of bioinformatics and its Applications
CO2 Difference between databases and various biological databases
CO3 Performing data storage methods and various formats.
CO4 Understanding sequence alignment and types of sequence alignment
Discuss about the basics of gene expression and understanding the difference between pattern finding
CO5
and regular expression
CO6 Deduce the evolutionary relationships between the sequences by generating a phylogenetic tree.
MITBIO/MITADT University
ClustalW
• The underlying concept is that groups of
sequences are phylogenetically related.
If they can be aligned then one can
construct a tree.
• Step 1-pairwise alignments
• Step 2-progressive alignment
• Step 3-create a guide tree
Sanket Bapat
Parts of a phylogenetic tree
Branch
Node
Root
Ingroup
Outgroup
Sanket Bapat
Phylogenetic trees diagram the evolutionary
relationships between the taxa
Taxon B
Taxon C
Taxon A
(((B,C),A), (D,E))
Taxon D
Taxon E
((A,(B,C)),(D,E)) = The above phylogeny as nested parentheses
These say that B and C are more closely related to each other than either is to A,
and that A, B, and C form a clade that is a sister group to the clade composed of
D and E.
Sanket Bapat
Tree Terminology
Rooted trees: Has a root that denotes common ancestry
Unrooted trees: Only specifies the degree of kinship among taxa but not the
evolutionary path
Scaled trees: Branch lengths are proportional to the number of
nucleotide/amino acid changes that occurred on that branch
(usually a scale is included).
Unscaled trees: Branch lengths are not proportional to the number
of nucleotide/amino acid changes (usually used to illustrate
evolutionary relationships only).
Sanket Bapat
Two major ways to root trees:
By outgroup:
Uses taxa (the “outgroup”) that are
known to fall outside of the group of
interest (the “ingroup”). Requires some
Types of data used in phylogenetic
prior knowledge about the relationships inference:
among the taxa.
Character-based methods: Use the aligned characters, such
as DNA or protein sequences, directly during tree inference.
By midpoint or distance:
Distance-based methods: Transform the sequence data
Roots the tree at the midway point
into pairwise distances (dissimilarities), and then use the
between the two most distant taxa in
matrix during tree building.
the tree, as determined by branch
lengths. This assumption is built into
some of the distance-based tree
building methods.
Sanket Bapat
Methods
• Distance matrix
• Maximum parsimony
• Minimum distance
Sanket Bapat
Analyses
1. Choosing the sequence type
2. Alignment of sequence data
3. Search for the best tree
4. Evaluation of tree reproducibility
Sanket Bapat
Algorithms used for tree searching
• Exhaustive search: all possibilities → best tree → requires lots of time
and computer resources
• Branch and Bound: a tree is built according to the model given → the
tree is compared to the next tree while its constructed → if the first
tree is better the second tree is abandoned → third tree… → best
possible tree
• Heuristic Search: only the most likely options → saves time and
resources.
Sanket Bapat
Visualising trees
• Treeview
• You can change the graphic presentation of a tree
(cladogram, rectangular cladogram, radial tree,
phylogram), but not change the structure of a tree
Sanket Bapat
Disclaimer:
The content delivered here should be considered of utmost importance. However, it is
to be noted that, this material is not Stand-alone material for the fulfilment of the
course syllabus. The content in this presentation should only be used as an aid to
learning.
Books and other resources provided are suggested to be referred for exhaustive
understanding.
MITBIO/MITADT University
References:
References Book Name Library
Jin Xiong Essential Bioinformatics Ebook / Present in Library
Rastogi, S. C Bioinformatics: Concepts, Skills And Applications Present in Library
Bosu Thukral Bioinformatics: Databases, Tools and Algorithms Present in Library
Neelam Yadav Handbook to Bioinformatics Present in Library
MITBIO/MITADT University
The content is intended for internal use only, and the ownership belongs to the coordinator. It
should not be uploaded on any platform without proper authorization.
