The most time-consuming part of estimating a phylogenetic tree is acquiring the sequences that will be the tips of the tree. Today, I learned how to find related sequences, and what criteria I should consider as I decide which sequences to include. The BLAST search in the MEGA program is the primary tool for identifying sequences that are homologous to your sequence of interest, the query sequence, and I used it today to acquire sequences related to the E. Coli bacteria.
Here is a screenshot of all the DNA sequences I acquired in BLAST:
It took me some time to figure out how to correctly acquire sequences. When you enter the query sequence, BLAST pulls up all the related DNA sequences, but it's up to you to determine which results will actually be useful. Then, you have to click on each sequence of interest and go through a process in which you add the sequence to your list in the correct format. Since the book was written for an earlier version of MEGA than the one I have, it took a lot of trial and error to correctly acquire all the sequences.
I appreciate you sticking with the process. Learning new applications, especially challenging ones like this, is always challenging.
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