Phylogenetic Analysis

The branch of science that deals with evolutionary relationships is referred as phylogenetics. Prediction or assessment of evolutionary relationship is referred as phylogenetic relationship. The relationship is depicted as phylogenetic tree diagram to show the estimated pedigree analysis. It is also referred as cladistics. Cladistics deals with evolutionary relationship. Clades are a group of organisms which are derived from ancestors of their kind. They help in prediction of multiple phenotype characters, base pairs and amino acids in a sequential manner. Quiet a number of phylogenetic algorithms, computer programs and procedures are developed based on the availability of data structure and size. Benefits and pitfalls of phylogenetic analysis devise reliable datas.

Objectives of phylogenetic relationship

• Conceptual approach to reveal the underlying principles
• Correcting model
• Particular data retrieval
• Evolutionary history interferences
• DNA sequence analysis prediction
• Protein sequencing

Phylogenetic model

Assumptions

• Sequences are originated from specific type of resource and are correct
• They are homologous sequence
• Homologous sequences are aligned
• Depicts phylogenetic history of species
• Adequate taxa sampling data
• Sequence variation is predominant
• Variability in phylogenetic sequence

Additional assumptions

• Sequence are developed based on single stochastic process
• Position of sequence also depends on stochastic process
• Sequences are developed independently

Tree interpretation

Evolution of protein and gene can be determined by comparing homologous sequence. Sequences which are developed with or without any information on common activity are referred as homologous sequence.  Somehow or other, they are developed from common ancestors who possessed the same structure. Homologous sequence is of three types namely, orthologs by speciation, xenologs by horizontal gene transfer and paralogs by gene duplication.

Steps of Phylogenetic data analysis

Following are the four steps of phylogenetic analysis.

• Multiple sequence alignment: Phylogenetic criteria development, estimation of alignment parameter, structural analysis and mathematical optimization.
• Substitution model determination: Substitution rates between bases, amino acids
• Tree building: Distance based method are neighbor joining method, unweighted pair group method with arithmetic mean (UPGMA), Fitch Margollash, minimum evolution. Character based methods are maximum parsimony (MP), maximum likelihood (ML), searching for trees and rooting of trees.
• Evaluation of phylogenetic tree: Randomized trees by Skewness test, Randomized character data by permutation test, bootstrap, parametric bootstrap and likelihood ratio tests.

Softwares for phylogenetic analysis

Following softwares are available for phylogenetic analysis.

• PHYLIP (Phylogenetic Inference Package)
• PAUP (Phylogenetic Analysis Using Parsimony)
• FastDNAml
• PUZZLE or TREE-PUZZLE
• MACCLADE
• MOLPHY
• PHYLODENDRON
• Web based softwares: WEBPHYLIP, Phyloblast, Blast 2 and Orthologue Search Server