#mthdlgy

[bio3project-blog]

j. After the analysis, a new window will appear showing the results. Check the BIC column and the model to be used is the one with the lowest value. k. Back on the first window, click “Phylogeny” then “Construct/Test Maximum Likelihood Tree” and click “Yes” l. Another window will appear and set some options based on the following: Test of Phylogeny: Bootstrap method No. of Bootstrap Replications: 1000 Substitution Types: Nucleotides (DNA) or Amino Acid (Protein) Model/Method: Use the model from the result of the earlier analysis Rates among Sites: Use the result from the result of the earlier analysis m.   Click “Compute” then the analysis will begin n.   After some time (based on the “No. of Bootstrap Replications” and number of sequences), the constructed tree will appear and it will show two versions: Original and Bootstrap

[bio3project-blog]

f.   Press Ctrl+A then click “Alignment” and “Align by ClustalW” g. Based on the reference sequence, delete the excess bases on both ends h.  Click “Data,” “Phylogenetic Analysis,” then “Export Alignment” in FASTA format i. On the first window, click “Models” then “Find Best DNA/Protein Models” and click “Yes” and “Compute”