Phylogenetic tree introduction, types, Multiple sequence alignment

1. PHYLOGENETIC
ANALYSIS

2. PHYLOGENETIC ANALYSIS
 A phylogenetic analysis of a family of related nucleic acids or proteins sequences
is the determination of how a family might have been derived during evolution
 The evolutionary relationship among the sequences are depicted by placing the
sequences as outer branches of trees
 The branching relationship on the inner part of the tree reflect the degree to
which different sequences are related
 Two sequences that are very much alike will be located as neighboring outside
branches and will be jointed to a common branch beneath them
 The object of phylogenetic analysis is to discover all of the branching relationships
in the tree and the branch lengths

3.  Phylogenetic analysis of nucleic acids and protein sequences is presently and will
continue to be an important area of sequence analysis
 In addition to analyze changes that have occurred in the evolution of different
organisms the evolution of a family may be studied
 On the basis of analysis sequences that are most closely related can be identified
by their occupying neighboring branches on a tree
 When a gene family is found in an organism or group of organisms phylogenetic
relationship among the genes can help to predict which once might have an
equivalent function
 These functional predictions can then be tested by genetic experiments

4.  Phylogenetic analysis may also be used to follow the changes occuring in a rapidly
changing species such as virus
 Analysis of the types of changes within a population can reveal for example
whether or not a particular gene is under selection an important source of
information in application like epidemiology
 Phylogenetic analysis thus amounts to the study of evolutionary relationships
 Phylogenetics is also called as cladistics because the word clade- a set of
descendants from a single ancestor is derived from the Greek word for branch

5. 3 BASIC ASSUMPTIONS OF CLADISTICS
 Any group of organisms is related by decent from a common ancestor
 There is a bifurcating pattern of cladogenesis
 Change in charactereristics occur in lineages over a time this is a necessary
condition for cladistics to work
 The resulting relationship from cladistic analysis are most commonly represented
by phylogenetic tree

6. PHYLOGENETIC TREE
 A clade is a monophyletic taxon . Clades are groups of organizers or genes that iclude the most
common ancestor of all or its members and all od the descendants of that most recent common
ancestor
 A taxon is any named group of organisms but not necessarily a clade
 In some analysis branch length corresponds to divergence
 A node is a bifurcating branch point
 Branch defines the relationships between the taxa In terms of descent and ancestory
 Topology is the branching pattern
 Branch length is often represents the number of changes that have occurred in the branch
 Root is a common ancestor of all taxa
 Distance scale represents the number of differences between sequences

8. TREE STYLES
 This offers the choice of tree diagram un rooted or rooted forms of cladogram etc
 Cladogram
nodes are connected to other nodes and to tips by straight line going
directly from one to another
this gives v shaped appearance

9. CURVOGRAM
 Nodes are connected to other node and to tips but a curve which is one forth of an
ellipse starting out horizontally and the curving upwards to bacame vertical

10. PHENOGRAM
 Nodes are connected to other nodes and to other tips by horizontal and then vertical
line
 This gives particularly precise idea of horizotal levels

11. EUROGRAM
 So called it is a version of cladogram popular in Europe
 Nodes are connected to other nodes and to tips by a diagonal line that goes
outwards and goes at most one third of the way up to the next mode that turns
sharply straight upward and vertical

12. swoopogram
 This option connects two node or a node and a tip using two curves that
are actually each one quarter of an ellipse
 The first part starts out vertical and then bands over to become a
horizontal
 The second part Which is at least one third of the total starts out
horizontal and then bends up to become vertical
 The effect is that two lineages split apart gradually then more rapidly then
both turn upwards

15. Applications of multiple sequence alingment
 Structure prediction
a multiple sequence alignment is an gives you the almost perfect protein
or RNA secondary structure some times it helps even with 3d structure
 Protein family
a multiple sequence alignment can help you to decide that your protein is
a member of a known protein family or not
 Pattern identification
by looking at conserved regions or sites you can identify which region is
responsible for functional site

16.  Domain identification
by looking at a file you can extract profiles to use them against
databases
 Dna regulatory element
you can use this to identify dna regulatory elements such as binding sites
 Phylogenetic analysis
by carefully picking related sequences you can reconstruct a tree using
sequences that are related