4 - Central Institute of Brackishwater Aquaculture

National Workshop-cum-Tra~ning on Biolnformatics and Information Management in Aquaculture
RECONSTRUCTION OF PHYLOGENETIC TREE USING
ONLINE TOOLS
All the morden biology is built upon the foundation of evolutionary theory and it
is impossible to evaluate relationships among sequences without taking into
consideration the way these sequences have been modified over time. Molecular
Phylogenetics deals with the study of evolutionary relationships among
organisms using molecular data like DNA, Protein sequences, transposable
elements and molecular markers. Similarity searches and multiple alignments of
sequences naturally lead to the question "How are these sequences related" and
more generally: "How are the organisms from which these sequences come
related". Sequence analysis of biological data is based on some evolutionary
principles which state that group of similar organisms descended from a common
ancestor.
Both nucleotide data and amino acid data can be used to generate phylogeny
and there has been much debate about which is the best. The main argument of
using amino acid data to infer phylogeny that there are 20 characters in
comparison to 4 characters and also the alignment of amino acid sequence data
is easier than DNA sequence data. A umber of evidences, which supports the
reconstruction of phylogeny from protein sequences, are very much useful than
DNA sequence [I].
Codon bias
Long time Horizon
Advantages of translation of DNA into corresponding protein sequences
Nature of sequence divergence in protein
Proteins have different rate of evolution
Introns and the noncoding DNA
Multigene families
Protein is the unit of selection
RNA editing
But it is advisable to analyse both data sets (DNA and protein) in favorable
condition.
As for a group of species or taxa that are relatively close in time or that are
closely related (like viral proteins or vertebrate enzymes) DNA-based analysis is
probably a good way to go, since problems as differences in codon bias or
saturation of the third position of codons can be avoidable in this case. It is
nevertheless strongly recommended to carry out an analysis on the protein data
as well.
' Correspondence: Su jya Narayan Rath, Asst.Professor; Dept. Bioinformatics, CPGS,
Orissa University of Agriculture & Technology; Bhubaneswar-751003;
snr-bioinfoQrediffmail.corn
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