Tools of phylogeny

1. Submitted By- Neha kumari
Roll no.-CUHP18ZOO17
SUBMITTED TO
MISS EKTA
GULERIA
CENTRAL UNIVERSITY
OF HIMACHAL
PRADESH

2. WHAT IS PHYLOGENY
PHYLOGENY - It is the evolutionary
history of a taxonomic group of organisms.
 It is closely related branch of science that make use of
phylogenetic tree diagrams to study evolutionary
history and relatedness among various group of
organisms is phylogenetics.

3. GOALS OF PHYLOGENY
 GOAL- Relationship between species, populations,
individual organisms.
 RESULT- Tree present as collection of nodes and
branches .
 Branch length shows---- Evolutionary time.

4.  Trees may be
 1 )Bifurcating
 2)Multifurcating
 ON THE BASIS OF BRANCH LENGTH
 Trees are of 3 types
1) Scaled tree
 2)Additive tree
 3)Unscaled tree

5. TOOLS FOR PHYLOGENETICS
DISTANCE BASED
a)Dnadist
b)Protdist
c)Fitch
d)Kitch
e)Neighbour
 CHARACTER BASED
 a)Dnamove
 b)Protpars

6.  Dnadist : is the phylip program for computing distances among DNA
distances.
 Protdist: is the program for computing distances for protein distances.
 Fitch: it estimates branch length assuming additivity of branch length
using FITCH MARGOLISH method .here molecular clock is not
assumed.
 KITCH: In this method ,it is quite similar to fitch. But it assumes a
molecular clock.
 Neighbour: it estimates the phylogeny using a neighbour joining or
UPGMA method.

7. METHODS TO BUILD A TREE
 UPGMA
 NEIGHBOUR JOINING
 DISTANCE BASED
 MAXIMUM PARSIMONEY
 MAXIMUM LIKELIHOOD METHOD

8. METHOD
 Choose a set of related sequence
 Obtain multiple sequence alignment
 Is there any sequence similarity
YES NO
Is there clearly
recognisable
sequence similarity
Maximum
parsimoney
Yes No
Distance based
method
Maximum
likelihood method

9.  The main distance based method include the UPGMA (
Unweighted pair Group Method With Airthmatic Mean)
and Neighbour joining method (NJ)
 Distnace based method method are used for the analysis of
large sequence.
 These methods use number of amino acids, changes
between the sequence .
 example: we can calculate the amino acid similarity
between each pair of protein in the multiple sequence
alignment.

10.  Dog and rabbit beta-globin are very closely related and
will be placed closed in a tree.
 Insect globin and soyabean globin are more distant
than the other sequence and are placed far away on the
tree.

11. UPGMA
 It is a sequential clustring algorithm.
 Pairwise distance between sequence are computed
and phylogenetic tree is built in a stepwise manner.
 Identify among all that are more similar to each other
&then treat them as a new single branch.
 In this we identify highest similarity among all

12. NEIGHBOUR JOINING METHOD
 It is an algorithm for constructing phylogenetic tree
 Once a distance measurement is done between a set of
sequences has been determined a neighbour joining
algorithm will find the two closest group
 Then look for next closest ,until all sequences are fit
into a tree.

13. MEGA
 It is a useful software in constructing phylogeny and
visulising them and also for data conversion.
 MEGA tree explorer is helpful in editing trees very easily.
 DENDROSCOPE: Helpful in visualizing large trees.
 PHYLOTREE.JS : It is a javascript based library to visualize
tree.
 One can upload trees using PHYLOTREE.JS.
 It is good for comparison of trees.

14.  TREE VIEW: Software to view the phylogenetic tree
with the provision of changing view.
 JS TREE: An open source library for viewing and
editing phylogeny tree for presentation improvement.
 PHYLIP: A package for phylogenetic studies.
 PMMLA: Based on maximum likelihood method .
 MOLPHY: Molecular phylogenetic evolutionary tool
based on maximum likelihood method.
 MEGA : Use to study the evolutionary closeness.

15.  TREE TOP: Phylogenetic tree prediction
 TREE OF LIFE: Information about phylogeny and
biodiversity.
 TREEGEN: Tree genration from distance data.

16. CHARACTER BASED
 Dnamove :It perform parsimoney and compatiblity
interactively.
 Protpars: It is based on the number of mutations to
change a codon for amin acid 1 to change a codon for
amino acid 2 for non synonymous changes only.

17.  With
gratitude .