Lab 7

For Lab 7, I practiced using phylogenetic tree analysis methods on 10 of the DNA sequences from my DNA isolation project earlier this semester. First, I ran the Jmodeltest program on my assembled BLASt hits in order to determine the best methods for analysis; the AIC gave HKY as the best molecular model, whereas BIC turned up H80. Next, I made a series of phylogenetic trees using different programs to test them out. First, I made a MrBayes tree using the HKY85 model. This gave back an identity suggestings that Red DrumĀ (Sciaenops ocellatus) was the most likely ID for my fish. Next, I did a Maximum likelihood tests with RAxML Bootstrapping, followed by one with PHYML bootstrapping. Both gave similar results as MrBayes, but with less support of side trees. Both gave weak posterior distributions, likely due to insufficient sample sizes.

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