phylogenetic analysis, tools and uses...part 1

Phylogenetics:-

- Phylogenetics is the study of the evolutionary history of living organisms using treelike

diagrams to represent pedigrees of these organisms.

Phylogenetic programs:-

Phylogenetic tree reconstruction is not a trivial task. Although there are numerous

phylogenetic programs available, knowing the theoretical background, capabilities, and

limitations of each is very important.

 PAUP* (Phylogenetic analysis using parsimony and other methods, by David Swofford,

http://paup.csit.fsu.edu/) is a commercial phylogenetic package.

 Phylip (Phylogenetic inference package; by Joe Felsenstein) is a free multiplatform

comprehensive package containing thirty-five subprograms for performing distance,

parsimony, and likelihood analysis, as well as bootstrapping for both nucleotide and amino

acid sequences.

 TREE-PUZZLE is a program performing quartet puzzling.

 PHYML (http://atgc.lirmm.fr/phyml/) is aweb-based phylogenetic programusing the GA.

It first builds an NJ tree and uses it as a starting tree for subsequent iterative refinement

through subtree swapping.

 MrBayes is a Bayesian phylogenetic inference program.

 MEGA Software for statistical analysis of molecular evolution. It includes different tree

visualization features

 Dendroscope An interactive viewer for large phylogenetic trees and networks

 NJplot Interactive tree plotter, re-roots, exports as PDF

MEGA (Molecular evolutionary genetics analysis):-

is a bioinformatics tool used for

genome analysis of molecular sequences to measure evolutionary distance for the

construction of phylogenies. MEGA software package was designed at the Pennsylvania State

University lab under the supervision of Masatoshi Nei. This tool was designed to extract

valuable information from nucleotide or protein sequence for statistical assessment and

biological data mining.

For the purpose of comparative genome analysis MEGA performs the following:

1. Sequence alignments

2. Evolutionary distance measurements

3. Phylogenetic tree building methods

4. Phylogenetic tree evaluation

5. Genes/Domains identification

6. Selection confirmation

7. Implementing sequence statistics

Step 1: sequence retrieval

Building sequence alignments involves many steps including acquiring sequences from

databanks using browsing facility. Homologous sequences are BLASTed by using either gene

name or accession number or a query sequence etc.

Step 2: Sequence alignment

By selecting add to alignment option, MEGA exports the sequences automatically to the

alignment explorer for producing multiple sequence alignments. Alignment explorer provides

two approaches using ClustalW through which data could be displayed as DNA sequence and

translated amino acid.

Step 3: Tree estimation

There are several tree estimation methods given below.

Distance based methods such as UPGMA and Neighbor-Joining (NJ) begins with

placing all the taxas in a single node and then separates with each repetition. In this way pair of

nodes are selected which are grouped at each iteration in order to reduce the overall branch

length. However mutation rates are not constant.

On the other hand character based methods such as parsimony and probalistic methods

selects the tree with the minimum number of alterations as the preferred tree by identifying and

estimating the total number of changes at each informative site for each possible tree.

Step 4: Bootstrapping

It is important to conduct statistical test for evaluating phylogenetic tree. Therefore

MEGA runs a statistical re-sampling process called bootstrapping to check trees reliability by

measuring the probability of branch recovery if the taxa were sampled again. Its values are

typically from 1000 repeated calculations and values >70% is acceptable.

Step 5: Phylogenetic tree exploration

Constructed phylogenetic trees can be visualized in numerous ways such as topologies

without branch length e.g. Cladogram or with estimated branch length e.g. Phylogram or in

linearized fashioned by means of tree explorer.