This video tutorial, presented by Ferdians Ciptono, demonstrates the step-by-step process of constructing a phylogenetic tree. The guide begins by retrieving nucleotide sequences for fish growth hormones (specifically for Gar/Leptisosteus species) from the NCBI database and converting them to FASTA format. These sequences are then imported into the MEGA (Molecular Evolutionary Genetics Analysis) application for sequence alignment using the Cluster method. Finally, the aligned data is used to construct and visualize a phylogenetic tree, showcasing the evolutionary relationships among the selected species, before saving the resulting tree image.
Creating a Phylogenetic Tree: A Step-by-Step Guide
0:00 Introduction: Ferdians Ciptono introduces himself and outlines the video's purpose: to guide viewers through the process of creating a phylogenetic tree.
0:16 Accessing NCBI for Gene Sequences: The first step involves navigating to the National Center for Biotechnology Information (NCBI) website.
0:25 Searching for Nucleotide Data: Within the NCBI portal, the "Nucleotide" database is selected, and the search term "Fish Growth Hormone" is entered.
0:53 Filtering and Selecting Species: The search results are filtered to specifically find sequences related to "Gar" or "Leptisosteus" species.
1:17 Downloading FASTA Sequence: The selected nucleotide sequence data is then downloaded in FASTA format, which is essential for bioinformatics analysis.
1:35 Importing Data into MEGA App: The downloaded FASTA file is opened using the MEGA (Molecular Evolutionary Genetics Analysis) software.
1:47 Initiating Sequence Alignment: In MEGA, the process for aligning sequences begins by selecting "Align" and then "Edit Build Alignment," followed by choosing to "Create New Alignment" for DNA sequences.
2:25 Editing and Trimming Sequences: The imported sequences are edited within MEGA, with non-essential portions manually deleted to refine the dataset for alignment (demonstrated by skipping lengthy sections for brevity).
2:48 Performing Cluster Alignment: The alignment of the trimmed sequences is executed using the "Alignment by Cluster method."
4:36 Saving Aligned Data: The completed sequence alignment is then exported and saved in the MEGA format for further analysis.
5:25 Constructing the Phylogenetic Tree: The saved alignment file is used to construct the phylogenetic tree by selecting "Phylogeny" -> "Construct/Test Neighbor-Joining Tree" in MEGA.
5:47 Visualizing the Tree: The resulting phylogenetic tree is displayed, illustrating the evolutionary relationships between various fish species (e.g., Acher, Lengusgar, Bovine, Paddlefish).
6:14 Saving the Tree Image: The generated phylogenetic tree is saved as a PNG image file for documentation or presentation.
6:40 Conclusion: The tutorial concludes with a thank you to the viewers and an apology for any potential errors.