This video tutorial, presented by Ferdiansyah Hilmi Ciptono, demonstrates the process of creating a phylogenetic tree using DNA sequences. The guide covers retrieving gene sequences from the National Center for Biotechnology Information (NCBI) database, specifically focusing on "fish growth hormone" for various fish species (e.g., Gar/Leptisode). These sequences are then imported into MEGA 11 software, aligned using the Cluster W method, manually trimmed for consistency, and finally used to construct a phylogenetic tree via the Neighbor-Joining method. The resulting tree, illustrating evolutionary relationships, is then saved as an image.
Tutorial: Creating a Phylogenetic Tree in MEGA 11
0:02 Introduction: Ferdiansyah Hilmi Ciptono (NIM C1401231113) begins a tutorial on how to create a phylogenetic tree.
0:16 Searching NCBI: The first step involves opening the National Library of Medicine (NCBI) website, selecting the "Nucleotide" database, and searching for "fish growth hormone."
0:51 Selecting & Downloading Sequences: The presenter demonstrates selecting specific fish sequences, such as "gar" or "leptisode." Once a desired sequence is found, it is downloaded by selecting "Send to," then "File," choosing "FASTA" format, and clicking "Create File."
1:35 Initializing MEGA 11: The tutorial proceeds to open the MEGA 11 application.
1:44 Creating a New Alignment: In MEGA 11, the user navigates to "Align," selects "Edit/Build Alignment," chooses "Create New Alignment," confirms with "OK," and then selects "DNA" as the data type.
2:02 Importing Sequences: The downloaded FASTA file containing the gene sequences is imported into the alignment editor via "Edit" > "Insert Sequence from File."
2:28 Aligning Sequences: All imported sequences are selected (Ctrl+A), and then aligned using "Alignment" > "Align by Cluster W."
3:09 Trimming Sequences: A critical step involves manually identifying the common start and end points of the gene sequences across all entries and trimming (deleting) the non-essential or divergent parts from both the beginning and the end for better alignment.
4:26 Exporting Alignment: After trimming, the refined alignment is exported in MEGA format by going to "Edit" > "Export Alignment" > "Mega Format" and saving the file.
5:18 Constructing the Phylogenetic Tree: Back in the main MEGA 11 window, the user selects "Phylogeny" > "Construct/Test Neighbor-Joining Tree" and then selects the previously saved MEGA alignment file.
5:45 Viewing the Tree: The phylogenetic tree is displayed, showing the evolutionary relationships between the included fish species (e.g., Acher, Sterin, Lengusgar, Bovine, Paddlefish).
6:03 Saving the Tree Image: Finally, the generated phylogenetic tree is saved as a PNG image by selecting "Image" > "Save as PNG."
6:38 Conclusion: The tutorial concludes with a thank you from the presenter.