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It has been our endower to present and explore different steps involved in the construction of a phylogenetic tree using online services. The application of different bioinformatic tools is necessary for the realization of the desirable results. A stepwise construction strategy using on line ClustalW is proposed with suitable application. The method can hope fully will aid the reader to construct the phylogenetic tree. Construction of phylogenetic tree is useful for comparison of homology of functional proteins in one species and between species.
Tree representation of the family history of set of sequences that share a common ancestor is called a Phylogenetic Tree. A phylogeny tree shows the connection among various organisms and weight of the branches in the tree indicates time between evolutions of different organisms.
Uses of Phylogenetic Tree
• Determining the relatives of the organisms and interested.
• Identify the functionality of a gene.
• Trace the origin of a gene.
1.1. Retrieving Protein sequence using major Protein databases.
Major Protein databases are
Protein Information Resource(PIR)
1.1.1. Open the link at to
1.1.2. Type required protein/gene sequence name in the Gene name window , and click the Submit Query button.
1.1.3. Select the required gene from given result and click.
1.1.4. To get the FASTA format, Click the FASTA format button , on the extreme right of the entry.
1.1.5. Save the Sequence into your PC.
1.2. Retrieving DNA sequence using major Nucleotide Sequence databases.
Major Nucleotide Sequence databases are
• European Molecular Biology Laboratory (EMBL)
• GenBank (National Center for Biotechnology Information, NCBI)
• DNA databank of Japan (DDBJ)
2.1. Open the link at to www.ncbi.nlm.nih.gov/BLAST
2.2. Click the Standard Nucleotide-nucleotide BLAST[blastn]/Standard Protein-Protein BLAST[blastp]
Ex: Click Standard Protein-Protein BLAST[blastp]
2.3. Open the Saved FASTA-formatted sequence(Protein/DNA) from the PC
2.4. Copy and Paste into the BLAST Searching window
2.5. Deselect the Do CD-Search box
2.6. If you use Protein Sequence don't change the Choose Database setting, because the nr (for non redundant) is the default protein database
2.7. Click the BLAST! Button
2.8. Click the Format button
2.9. When the results page appear, scroll down the page until you reach along list of sequences and save all these sequences into your PC
To compute your multiple sequence alignment, any of the following can be used
• ClustalW :
• Dialign :
• Tcoffee :
Steps to produce multiple sequence using EBI ClustalW server
3.1. Open the link at the EBI ClustalW server at
3.2. Paste the collected sequences from the sequence window
3.3. Use Output format pull-down menu to set the selection of choice
3.4 Choose Input from the Output Order pull-down menu. When output order set to input, ClustalW outputs your sequence in their original order. If the output order is set to aligned, the sequence appears in the order of they are aligned
3.5. Click the Run Button at the bottom of page
3.6. Save your results. Results come in three sections. First one is Pairwise section, second one is the multiple Alignment and third one is guide tree
Use the following methods to construct the Phylogenetic Tree
• ClustalW
• Phylip
Steps involved in a phylogenetic tree using online EBI ClustalW server
4.1. Open the link at the EBI ClustalW server at
4.2. Paste your Multiple alignment into sequence window
4.3. Choose NJ from Phylogenetic Tree: Tree Type drop down menu
4.4. Choose On from Correct Dist. Drop-down menu
4.5. Choose On from the Ignore Gaps drop-down menu
4.6. Choose Phylogram from the Tree drop-down menu
4.7. Click the Run Button and view the tree
4.8. Results are saved
a. Point your browser to
b. Type Gene name Bche in Gene name window,Homo sapiens in Organism window and click the Submit Query button
c. http://www.expasy.org/cgi-bin/get-entries?db = sp & db = tr & DE = & G Nc = AND & GN = Bche & OC = Homo + sapie ns & wild = 1 & view = full & num = 100
d. Select the required gene from given result. For Ex: P06276 and get the FASTA format and save
e.
a. Point your browser to
b. Paste P06276 FASTA formatted sequence in the sequence window
c. Press Format Option if your request has successfully executed
d. Select required sequence and Save into your PC
a. Point your browser to the EBI ClustalW server
b. Paste colleted sequences in the sequence window
c Click the Run Button at the bottom of page
d. Save your results
a. Point your browser to the EBI ClustalW server
b. Paste Multiple Sequence alignment into sequence window
c. Choose NJ from Phylogenetic Tree: Tree Type drop down menu
d. Choose On from Correct Dist. Drop-down menu,Choose On from the Ignore Gaps drop-down menu,Choose Phylogram from the Tree drop-down menu and Click the Run Button and view the tree
For phylogenetic tree construction, the essential performance parameters have been discussed here in detail to provide guidance to computational biologists. In particular, the stepwise discussion strategy is a very attractive goal, and this methodology, which, if appropriately used, can solve several problems and constitutes a powerful tool in the hands of researchers. The aim of this article, with application to Phylogenetic tree construction of butyrylcholinesterase has been contribute to a further research studies for homology comparison of functional proteins in species.
This work was supported by IIT up gradation grants of AUCE (A).