This document provides an overview of molecular phylogenetic analysis. It discusses how phylogenetic analysis uses molecular techniques to infer evolutionary relationships among organisms or genes. It describes common computational methods for phylogenetic analysis, including assembling and aligning datasets, and building phylogenetic trees. It also summarizes some online tools for phylogenetic analysis and discusses applications of molecular phylogenetics in different biological disciplines.

1. Assignment
Submitted to
Farhana Sharmin
Department. of CSE
Daffodil International University
Submitted by:
Ashik-E-Rabbani (161-15-7093)
Samsil Arefin (161-15-7197)
Arman Fajlur Rahman (161-15-6991)
Hasnain Habib Rakin (161-15-7379)
Md. Mazharul Islam (151-15-4793)

2. Evolution Phylogenetic
Abstract
Molecular phylogenetic applies a combination of molecular and statistical techniques to infer
evolutionary relationships among organisms or genes. This review assignment provides a general
introduction to phylogenetic and phylogenetic trees, describes some of the most common
computational methods used to infer phylogenetic information from molecular data, and
provides an overview of some of the many different online tools available for phylogenetic
analysis. In addition, several phylogenetic case studies are summarized to illustrate how
researchers in different biological disciplines are applying molecular phylogenetic in their work.
Keywords: Phylogenetic; Phylogenomics; morphology; Genome-scale; and systematics.
INTRODUCTION TO MOLECULAR
PHYLOGENETIC
The similarity of biological functions and molecular
mechanisms in living organisms strongly suggests
that species descended from a common ancestor.
Molecular phylogenetic uses the structure and
function of molecules and how they change over
time to infer these evolutionary relationships. The
primary objective of molecular phylogenetic
studies is to recover the order of evolutionary
events and represent them in evolutionary trees
that graphically depict relationships among species
or genes over time.
PHYLOGENETIC ANALYSIS
Phylogenetic analysis Phylogenetic analysis show
the developmental connections among groups of
living forms, or among a group of related nucleic
acid or protein sequences. Phylogenetic
connections among genes can help to conclude
which ones may have comparative functions.
UNDERSTANDING PHYLOGENETIC TREE
OF LIFE
Phylogenetic trees are composed of branches, also
known as edges that connect and terminate at
nodes. Branches and nodes can be internal or
external (terminal). The terminal nodes at the tips
of trees represent operational taxonomic units
(OTUs). OTUs correspond to the molecular
sequences or taxa (species) from which the tree
was inferred. Internal nodes represent the last
common ancestor (LCA) to all nodes that arise from
that point. Trees can be made of a single gene from

3. many taxa (a species tree) or multi-gene families
(gene trees).
TREES AND HOMOLOGY
Evolution is shaped by homology, which refers to
any similarity due to common ancestry. Similarly,
phylogenetic trees are defined by homologous
relationships. Paralogs are homologous sequences
separated by a gene duplication event. Orthologs
are homologous sequences separated by a
speciation event (when one species diverges into
two). Homologs can be either paralogs or
orthologs.
STEPS IN PHYLOGENETIC ANALYSIS
Although the nature and scope of phylogenetic
studies may vary significantly and require different
datasets and computational methods, the basic
steps in any phylogenetic analysis remain the same:
assemble and align a dataset, build (estimate)
phylogenetic trees from sequences using
computational methods and stochastic models,
and statistically test and assess the estimated trees.
The first step is to identify a protein or DNA
sequence of interest and assemble a dataset
consisting of other related sequences. There are a
number of free, online tools available to simplify
and streamline this process. DNA sequences of
interest can be retrieved using NCBI BLAST or
similar search tools. When evaluating a set of
related sequences retrieved in a BLAST search, pay
close attention to the score and E-value.
A high score indicates the subject sequence
retrieved with closely related to the sequence used
to initiate the query. The smaller the E-value, the
higher the probability that the homology reflects a
true evolutionary relationship, as opposed to
sequence similarity due to chance. As a general
rule, sequences with E-values less than 10-5 are
homologs of a query sequence. ClustalW is
currently the most mature and most widely used.
Methods of Analyzing
 Assemble and Align Datasets
 Distance-Matrix Methods
 UPGMA Method
 Discrete Data Methods
 Maximum Likelihood
PHYLOGENETIC ANALYSIS TOOLS
There are several good online tools and databases
that can be used for phylogenetic analysis. These

4. include PANTHER, P-Pod, PFam, TreeFam, and the
PhyloFacts structural phylogenomic encyclopedia.
Each of these databases uses different algorithms
and draws on different sources for sequence
information, and therefore the trees estimated by
PANTHER, for example, may differ significantly
from those generated by P-Pod or PFam. As with
all bioinformatics tools of this type, it is important
to test different methods, compare the results,
then determine which database works best
(according to consensus results, not researcher
bias) for studies involving different types of
datasets.
In addition, to the phylogenetic programs already
mentioned in this paper, a comprehensive list of
more than 350 software packages, web-services,
and other resources can be found here:
APPLIED MOLECULAR PHYLOGENETIC
Molecular phylogenetic studies have many diverse
applications. As the amount of publically available
molecular sequence data grows and methods for
modeling evolution become more sophisticated
and accessible, more and more biologists are
incorporating phylogenetic analyses into their
research strategy. Here’s a sampling of how
molecular phylogenetics might be applied.
LATEST RESEARCH
Phylogenetics is the attempt to reconstruct the
evolutionary relationships between species.
Historically, this was done using quantitative
morphological data, but modern methods rely
more heavily on DNA sequence data. Top latest
Research topics are below:
[1] A new stem sarcopterygian illuminate’s
patterns of character evolution in early bony
fishes. [ Jing Lu, Sam Giles]
[2] Evolutionary conservation and functional
divergence of the LFK gene family play important
roles in the photoperiodic flowering pathway of
land plants [ By Ling Lu, Yuanqi Wu.]
[3] A genomic perspective of the pink-headed
duck Rhodonessa caryophyllaceous suggests a
long history of low effective population size. [By
Per G. P. Ericson]
[4] Resolving kangaroo phylogeny and overcoming
retrotransposon ascertainment bias.
OUR AIM AND FUTURE SCOPE
Phylogenetic, Phylogenomics, and Systematics is
dedicated to the use of phylogenies as interpretive
frameworks for species discovery, establishment of
biological classifications, comparative genomics,
and testing hypotheses about evolutionary
processes. As such, we recognize that studies of
evolutionary complexity require a synthesis of
appropriate information from various levels of
organization, ranging from molecules to the
morphology of extant and fossil forms. Such
syntheses provide better resolution of
relationships among taxa, thus enhancing

5. classifications. They also allow for more accurate
estimation of divergence times and for the
examination of various evolutionary processes (e.g.
functions of coding and noncoding sequences;
speciation; convergence and homology; and the
origin of complex traits). We encourage
submissions of phylogenetic investigations of all
branches of the Tree of Life. Additionally, we
welcome manuscripts on analytical and
computational methodologies that bring clarity
and/or new insights and advancements to the field
of phylogenetics, phylogenomics, and systematics.
CONCLUSION
Phylogenetics is a broad, diverse field with many
applications, supported by multiple computational
and statistical methods. The sheer volumes of
genomic data currently available (and rapidly
growing) render molecular phylogenetics a key
component of much biological research. Genome-
scale studies on gene content, conserved gene
order, gene expression, regulatory networks,
metabolic pathways, functional genome
annotation can all be enriched by evolutionary
studies based on phylogenetic statistical analyses.
REFERENCES
[1] Rosen MJ and Kunjappu JT (2012). Surfactants
and Interfacial Phenomena (4th ed.). Hoboken,
New Jersey: John Wiley & Sons. p. 1. ISBN 1-118-
22902-9
[2] Hodge T, & M. J. T. V. Cope. 2000. a myosin
family tree journal of cell science. Woese C. R.
1998.
[3] Felsenstein J (2004) Inferring phylogenesi
s sinauer associated Sunderland.
[4] Hodge T, Cope MJ (2002) A myosin family tree.
[5] Maher B. A. 2002 Uprooting tree of life.