Bioinformatics and Functional Genomics Student ID: 21485094
Lecturer: Dr. Obed Brew Beatriz Manso
1
COMPLEX PHYLOGENETIC ANALYSIS WITH MEGA
Phylogenetic analyses are performed to answer questions like: What are the evolutionary
relationships or histories among my species/individuals/genes of interest? How do sequences
evolve? Can I better describe processes of sequence evolution with a mathematical model? While
phylogeny (also known as a tree) is an explanation of how sequences evolved, their genealogical
relationships, and therefore how they came to be the way they are today, a phylogenetic tree is
constructed to estimate the relationships among taxa (or sequences) and their hypothetical common
ancestors (Nei and Kumar 2000; Felsenstein 2004; Hall 2011).
A complete phylogenetic experiment requires four distinct steps:
1. Identify and acquire a set of homologous DNA or protein sequences
2. Align those sequences
3. Estimate a tree from the aligned sequences
4. Present that tree in such a way as to clearly convey the relevant information to others. The
aim of this experiment is to provide opportunity for you to examine and successfully
complete all the required steps involved in phylogenetics analysis to a
professional/industrial standard.
Perform BLAST from MEGA
1. Start MEGA, it opens the main MEGA window.
2. Go to menu and select Align
3. Choose Do Blast Search. This will open NCBI Blast
4. There is a large text box (Enter accession number . . . ) where you enter the sequence of
interest. Paste the query sequence directly into that box.
5. Click on the nucleotide blast (blastn) link from the BLAST page
6. Copy and paste or upload the pldaoseq sequence into the ‘Enter Query Sequence’ box.
7. Set Parameters as follows:
a. Choose "Nucleotide collection (nr/nt)" as the search database. NR is the "Non
Redundant" database, which contains all non-redundant (non-identical) sequences
from GenBank and the full genome databases.
b. In the section "Program Selection" select Optimise for "Somewhat similar sequences
(blastn)
8. Click BLAST to get your results and select a few sequences to add to your alignment and thus
to include on your phylogenetic analysis.
Bioinformatics and Functional Genomics Student ID: 21485094
Lecturer: Dr. Obed Brew Beatriz Manso
2
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