Phylogenetic Tree Construction

What can a phylogenetic tree tell you?

• Degree of similarity between species/sequences

• Evolutionary relationship between species/sequences

• The timing of evolutionary events

• All of the above

What is the golden standard for rooting a phylogenetic tree?

• Outgroup rooting

• Random rooting

• Midpoint rooting

• None of the choices

When is the use of Muscle Alignment preferred over ClustalW?

• For smaller datasets

• For distantly related sequences

• For closely related sequences

• None of the choices

What is the second step in constructing a phylogenetic tree?

• Phylogenetic inference

• Model Selection

• Data Preparation

• Multiple Sequence Alignment

Which public nucleic acid database is maintained by the National Institutes of Health?

• DDBJ

• EMBL

• GENBANK

What is the Accession code prefix for NCBI's non-coding reference sequences?

• NM

• NK

• NR

• NP

What is the threshold bootstrap value for a phylogenetic tree to have weak support?

• >50%

• <50%

• >70%

• <70%

How many bootstrap replicates is standard for constructing a phylogenetic tree?

• 1000

• 500

• 100

• 10000

When examining the statistical support of a phylogenetic tree, which generated tree should be used?

• Original Tree

• Bootstrap Consensus Tree

• Condensed Tree

When examining the fundamental evolutionary relationship given the data, which generated tree should be used?

• Original Tree

• Bootstrap Consensus Tree

• Condensed Tree