Choosing a Method for Phylogenetic Prediction

Contents
Phylogenetic prediction Chapter 9..............................................................................................................3
1. Phylogenetic........................................................................................................................................3
1.1. Definition:....................................................................................................................................3
1.2. Importance of phylogenetic.........................................................................................................5
1.3. Important steps in phylogenetic Analysis....................................................................................6
1.4. Phylogenetic Applications............................................................................................................8
Table of Figure:
Figure 1 Phylogenetic analysis.......................................................................................................4
Figure 2 Phylogenetic elements....................................................................................................5
Figure 3 Potential applications of phylogenetic...........................................................................6
Figure 4 Major steps in phylogenetic analysis...............................................................................7
Figure 5 phylogenetic Potential applications................................................................................8
Figure 6 Life Tree.........................................................................................................................10
Figure 7 Relationship between different species........................................................................11
Figure 8 Rooted Tree...................................................................................................................13
Figure 9 Unrooted tree................................................................................................................14

Figure 10 The Point considering while selecting a method.........................................................15
Figure 11 Multiple sequence alignment......................................................................................17
Figure 12 Possible Tree................................................................................................................18
Figure 13 Alignment.....................................................................................................................19

Phylogenetic prediction Chapter 9
1. Phylogenetic
1.1. Definition:
“Phylogenetic analysis is the study of the evolutionary development of a species or a group of
organisms or a particular characteristic of an organism” as shown in figure 1
Figure 1 Phylogenetic analysis
Phylogenetic is the study of how different biological things, usually called species, individuals, or
genes, have changed over time (which may be referred to as taxa). Figure 2 below shows how
the most important parts of phylogenetics can be broken down into their parts.

Figure 2 Phylogenetic elements.
Most of the time, phylogenies research one of the following types of questions:
• How are the species, individuals, and genes I want to study related to each other in terms
of evolution?
• How do sequences evolve?
• Can I use a mathematical model to describe the process of sequence evolution more
accurately?
we can put together a phylogenetic tree by looking at the sequences of nucleotides or proteins
and putting that information together with what we know about how sequences have changed
over time, which is shown in an evolutionary model. This tells us more about how sequences
have changed over time, but it also lets us figure out what changes have happened in the past.
Because of this, we might be able to learn more about how evolution works and make more
accurate mathematical models of the process.
The phylogenetic analysis shows how a group of related sequences came to be. This helps us
understand how evolution works. The tree's branching structure shows how the sequences are

related to each other in terms of evolution. The length and nesting of these branches show how
similar any two given sequences are. The phylogenetic analysis aims to figure out how long the
tree's branches should be and how to arrange them best. The branches of a tree next to each
other show how closely related two sequences are to each other.
The quality of the multiple sequence alignment programs used is directly linked to how well
phylogenetic analysis works. The phylogenetic analysis starts with multiple sequence
alignments and works backward to group sequences into categories based on the patterns of
substitutions they share. This is how a phylogenetic tree can be made again. Take the fact that
two sequences are linked to each other. If you look at these two sequences together, you can
(partially) figure out what the original sequence was. When more sequences are similar, it is
easier to get more information that will help make a correct history of how things came to be
and how they changed over time.
1.2. Importance of phylogenetic
Phylogenetic is an important field because it helps us learn more about how genes, genomes,
species, and even molecular sequences change over time. By studying phylogenetics, learn how
the sequences got to where they are now, but we also learn general rules that help us predict
how the sequences will change in the future. This is very important, but it is also very valuable
in a lot of different ways as shown in figure 3.

Figure 3 Potential applications of phylogenetic
When a group of genes, also called a "gene family," is given, phylogenetic analysis can be used
to figure out which genes are most likely to do the same.
Used to keep track of changes in a species that is changing quickly, like a virus. Take the case of
the flu as an example. By doing phylogenetic analysis on the genes that change quickly,
predicting the most common flu strain for the next year and making a vaccine against it is
possible. Even though the prediction isn't always right, it does offer some protection.
1.3. Important steps in phylogenetic Analysis
There is no set way to finish a phylogenetic analysis because the methods we use depend a lot
on the context and circumstances, in the end. However, some major stages that you will almost
certainly go through, and Figure 4 gives a detailed look at these stages.

8
Figure 4 Major steps in phylogenetic analysis

1.4. Phylogenetic Applications
Figure 5 phylogenetic Potential applications
Some ways that phylogenetic can use
Classification: When it comes to putting things into groups, phylogenetic based on sequence
data gives us more accurate descriptions of how closely related things are than what we had
before molecular sequencing. The Linnaean system now uses phylogenetic to help classify
species that have just been found.
Forensics: Phylogenetic is used to look at DNA evidence in court cases to find out if someone
has done something wrong. Here are some examples of these situations: if food has been
tainted, or if the child's father is unknown.
Identifying the origin of pathogens: There are two ways to find out more about a new outbreak
of an infectious disease: molecular sequencing technologies and phylogenetic approaches.
These methods can be used to find out where pathogens come from. This includes figuring out
what species the pathogen is related to and, as a result, what species is most likely to spread it.
This could lead to new ideas about how public health policy should be carried out.

Conservation: When conservation biologists are deciding which species they should work the
hardest to save from extinction, phylogenetic can help them figure out the best way to do this.
Computing and bioinformatics: Many of the algorithms made for phylogenetic have been used
to make software for other areas of study.