BUILDING a neighbor-joining tree in mega
MEGA is an extremely popular program for sequence analysis. MEGA is free to download from: http://www.megasoftware.net/
a. Start MEGA by double-clicking on the MEGA desktop icon
b. You can then choose File>Open A File/Session… >Select the file sequences.fasta from your Desktop >Open>Analyze>Nucleotide Sequences>OK >Yes>Invertebrate Mitochondrial>OK
c. You can then choose Phylogeny>Construct/Test Neighbor-Joining Tree…>Yes
d. In the Analysis Preferences window Options Summary tab choose the following options:
Test of Phylogeny | None
Substitution type | Nucleotide
Model/Method | p-distance
Substitution to include | d: Transitions + Transversions
Gaps/Missing Data Treatment | Pairwise deletion
Select Codon Positions | tick all (1st, 2nd, 3rd and Noncoding Sites)
a. Start MEGA by double-clicking on the MEGA desktop icon
b. You can then choose File>Open A File/Session… >Select the file sequences.fasta from your Desktop >Open>Analyze>Nucleotide Sequences>OK >Yes>Invertebrate Mitochondrial>OK
c. You can then choose Phylogeny>Construct/Test Neighbor-Joining Tree…>Yes
d. In the Analysis Preferences window Options Summary tab choose the following options:
Test of Phylogeny | None
Substitution type | Nucleotide
Model/Method | p-distance
Substitution to include | d: Transitions + Transversions
Gaps/Missing Data Treatment | Pairwise deletion
Select Codon Positions | tick all (1st, 2nd, 3rd and Noncoding Sites)
e. Click Compute to accept the defaults for the rest of the options and begin the computations. A progress indicator will appear briefly before the tree displays in the Tree Explorer.
f. To select a branch, click on it with the left mouse button. If you click on a branch with the right mouse button, you will get a small options menu that will let you flip the branch and perform various other operations on it. To edit the taxon labels, double click on them.
g. Change the branch style by using View>Tree/Branch Style.
h. Select View>Topology Only to display the branching pattern (without actual branch lengths on the screen).
f. To select a branch, click on it with the left mouse button. If you click on a branch with the right mouse button, you will get a small options menu that will let you flip the branch and perform various other operations on it. To edit the taxon labels, double click on them.
g. Change the branch style by using View>Tree/Branch Style.
h. Select View>Topology Only to display the branching pattern (without actual branch lengths on the screen).