BIO 253

ACTIVITY 1
Estimating a Phylogenetic
tree based on molecular
sequence data
By: Chale Noven G. Maravillas
 STEP 1: Enter the
desired species in BLAST

Note: if you have already a sequence stored in NCBI

(https://blast.ncbi.nlm.nih.gov), just use the Enter accession in the
“Enter Query Sequence” and the query subrange. But if you don’t have
any stored sequences in the NCBI then just enter the sequence using
the FASTA format or just simply upload the file.

STEP 2: Click BLAST

STEP 3: Results of the BLAST Search
STEP 3: Results of the
BLAST Search (graphic
summary)
STEP 3: Results of the BLAST Search (Alignments)
31 sequences that have the value of E value of ≤10^(-
3)
And query coverage criteria of ≥60%
STEP 4: Use BioEdit.
A piece of advise, use Bio Edit for faster editing of the sequence
since editing in MEGA 11 can be a little bit of a hassle. MEGA 11 will not
run it’s alignment tool or “alignment by muscle” if the sequences do not
have the same length of sequences

STEP 4: Use MEGA 11 for alignment of sequence.

MEGA 11 is faster than its older versions so I prefer using this.
Don’t worry it’s a free software.
STEP 5: alignment results in mega 7.

STEP 6: save the session.

trust me you need this if you don’t want to go back to square
one
STEP 6: save the session.
STEP 7: Open the File/Session you wish to construct a phylogenetic
tree.
See! That’s why I said that you need to save the session from your
aligned sequences. See STEP 6
STEP 8: Let’s Construct the Phylogenetic Tree. Please click
“PHYLOGENY”

STEP 9: Let’s Construct the Phylogenetic Tree. Please click

“Construct/Test Neighbor-Joining Tree”
STEP 10: Let’s Construct the Phylogenetic Tree. Please click “Yes”

STEP 11: Let’s Construct the Phylogenetic Tree. Please click “OK”
STEP 12: VOILÀ! Here’s your Phylogenetic Tree.

STEP 13: Save your Phylogenetic Tree. Please click “File”>“Save

Current Session”
STEP 13: Save your Phylogenetic Tree. Please click “Save”